Dr_Watso makes a good point about setting up your kit ergonomically--what's comfortable for you is the best way. However, sometimes your kit won't LET you set things up exactly the way you want. In my case, I like my snare rim to be on the same plane, more or less level with the adjacent toms, and each tom rim level with the toms on either side, except for my 16" floor tom, which has to be quite a bit lower than the 14" tom. This works best for me, because it reduces the amount of unwanted rim hits when doing various fills.
The problem is my toms are all deeper versions of Fusion sizes; 10 x 9, 12 x 10, 14 x 12. My 12" tom's depth means I have to position it higher than what would be perfect, so it won't scuff the bass drum. I'd prefer to have it flatter and lower, but then it wouldn't be level with the 10" or 14" and the snare.
But given the limitations of your kit specs, set things up the way that's most ergonomic for you.