Now, I have no idea what your room is like. So, I'm going to assume it's reasonably good. If that is the case, then you shouldn't have to worry about reflections from walls, but in terms of kit placement, you want to keep it away from walls and preferably under a high ceiling. If you have any walls that directly face each other, and any right angles for that matter, I would recommend throwing some treatment in. I often find a blanket works. Or an old mattress or anything soft and porous - Auralex foam is ideal (and designed for the purpose). If you haven't got access to any of this, a quick solution to prevent dodgy reflections in the overheads is to drape a blanket or duvet over the back of the capsules and drape it between them, so you've effectively covered the back (NOT THE FRONT) of the capsules with a blanket. The bass drum and snare are less critical, because they'll get more direct signal because of their proximity to the sound sources.
When you get the recording into your computer, obviously assign each microphone a different channel. I tend to work overheads, bass, snare, snare. Some work bass, snare, snare, overheads. Do it as you feel is fit, just make sure it makes some sense to you! Pan each of the overheads left and right, and pan the snare into the correct place of the stereo field. If it's slightly to the left of you, pan it, etc. Bass is usually central (there's an historical reason for this as well as the obvious stereo field reason, but it's just a nice factoid. Basically, bass takes up a bigger groove on vinyl, so having it central made sure it took up as little space as possible. Dull fact, I find it interesting).
EQing is a tricky business and you have to think in terms of SUBTRACTIONS as well as additions. Seeing as your overheads are probably going to be used for everything to some extent, it's necessary that their response is relatively even. Listen to the recordings and if anything is ridiculously wayward, first of all play with the mic placement. Getting a good recording in is the most important thing - trying to fix it with EQ is a work-around and doesn't produce as good a results. EQ is there to shape the sound, not to correct it - unless something has gone drastically wrong and there's nothing you can do to re-record.
Without being in person, it's hard to tell you what to do with the EQ, but generally speaking, a cut around 250Hz helps prevent muddiness, and a slight boost at the top end helps add some sibilance to the sound (and makes it sound a little 'airy' if you like). Seeing as tom toms work over the range of sounds, I'd suggest taking a little out just below the top (15Khz) and keeping the rest relatively flat. Obviously, small alterations can be made to the low-mid and high-mid as you feel fit, but it's very much a case of feel rather than giving you specific instructions. I tend to work on subtractions more than additions, because it gives you a greater scope for contrast. If you're only adding EQ, you're effectively just using half of its available range, right?
What also might help (and this is where things get interesting) is a little compression on the overheads, just to take the edge off the peaks. A low ratio is probably good, say 2:1, but be prepared to just drop the level of the overhead channel slightly, as compression can make it 'louder' overall. I say can. It's often misused to do just this... maybe a little reverb too if the sound you're getting is very dry (ie. you have the blankets over the backs of the mics!).
With the bass drum mic, you'll want a peak in the EQ below 100Hz, a dip at 250Hz (I'll explain this in a minute) and you'll probably want a slight rise around 2.5Khz for the attack of the beater. It's quite simple. When I say drop the 250Hz, there is one good reason for this - most instruments tend to have something happening at 250Hz or thereabouts - guitars do, drums do, bass guitars do, cellos do, pianos do. Just go through the list and think of an instrument that doesn't have 250Hz and you'll struggle. Unless we're talking about hammered dulcimers (micing those up is fun!). So, in short, the 250 can get very crowded. When you get a 'muddy' recording, it's usually around that kind of range that gets over-powered, so if you hear any muddiness, drop the 250ish and see what happens.
A little compression is good on the bass drum too. More compression than the cymbals, say 3:1 or more. Just play with it and see what you like - it helps make it more 'punchy'.
The snare is a little trickier. Basically it's EQ to preference as to tuning. Subtract what you don't want as opposed to adding all of what you do want. The top mic will probably sound reasonably ok with a bit of compression, maybe some reverb, but not too much! The relationship with the bottom mic is a tricky one and I would say that if you can get the sound you want out of the top mic, use that. A lot of the snare will be in the overheads too, so you'll want to use some of the overheads for the snare - using the snare mics just as embellishment, effectively. The bottom mic is tricky because first of all the sound it produces can be just 'rattly' and secondly, the phase relationship is tricky. Basically, phase is when the same signal reaches two different microphones at different times and when put together, cancel each other out. If you introduce the bottom snare mic into the mix and the snare starts sounding very weird (like a reduction in volume, or choked) invert the phase of the bottom mic. There's usually a button on the desk to do this, or on your interface - or even on Cubase. That should help. Again, slight EQ to preference, cut the 250. If you don't feel you need the bottom snare mic, don't use it. It just adds a little depth.
Now, when you've all got them sounding good individually (solo each one when you're playing around, forgot to mention that) it's now a job to get them sounding good together. By using subtractive EQ, this is more likely to happen straight away. Basically, the overheads are the bread and butter of your mix and the other mics are just embellishments or 'accent' mics to add a bit extra to what's already there. So, usually a little bias in favour of the overheads is in order. Just work to where you feel the sound is nicely balanced and don't be afraid to play around with the EQ on each individual piece if you feel something is too prominent. Remember as well, the louder you mix, the more the bass will be obvious, so work at a sensible level of volume! It might help at this point to group the drums together so that one slider controls the overall level. Also, sending the drums to a buss (a group send) might be a good idea, then you can add compression, reverb, etc to the overall group. Basically - you can start to treat the drums as two channels (stereo) rather than as a collection of individual instruments.
With the bass and guitar, there are various ways of doing it. You can choose to record directly into the desk using a DI (direct input) box or alternatively you can usually plug the guitar right in using a jack and actually increase the gain there to get a good signal level. I've used that method a few times and it works. Most Bass amps have a DI built into them with an XLR output - you could use that and if it's available, do. All this can go directly into the desk. One of my guitar amps actually has a 'line out' on it - if your guitarists' does, use that - it should provide a decent signal and you might not need any extra gain.
Alternatively, you could mic the individual cabinets. This is slightly trickier, because you're likely to get the drums into the sound if you're all playing together and it's probably simpler just to DI it all, even though it doesn't always sound as good as micing. If you are micing the cabinets, a dynamic mic (Shure SM57, etc) placed about 4 inches from the cabinet and slightly off-centre and below the cone is probably the most standard practice.
With regards to mixing the bass and guitar, it's really a matter of playing around until you get what you want. Don't be afraid to really compress the bass and make it work - but also be careful of muddiness - avoiding reverb helps with this. It might also be a good idea to record the band 'live' and then record the guitar and bass tracks over the live drum recording, taking away the original guitar and bass tracks. This is the method usually used when a Click track isn't being used. If you're recording as a band, you as the drummer ought to have the click in his ear, Cubase produces its own click, so it's simply a case of hooking up some headphones to the outputs on the Aardvark (via the mixer probably, just put the click into a separate channel). Remember my advice on subtractive EQing, it works wonders. It might also be preferable
When you're trying to record into Cubase, select the right input for each sound source according to the channel on the mixer. For instance, channel one on the mixer should be plugged into channel one on the interface and this will be selected as 'Input 1' on Cubase. (Or the equivalent). This will help you organise everything properly!
I'm not going to talk about mastering right now, because I could literally could go on all day about mastering, but suffice to say, when it comes to putting your mix to a stereo output, make sure that it doesn't clip. That is to say, the output is too high. Otherwise it gets bothersome and won't sound good. If necessary, reduce the volumes of each of the other instruments until you get it within reasonable parameters.
You didn't mention if you had vocals or not. If you have, tell me and I'll fill you in on the basics there. Seeing as you didn't mention them, I kept them out deliberately to avoid confusion.