Play along as many times as it takes......and then, something Steve Morse said awhile back.....also listen to the song while ironing your shirt, cooking breakfast....etc....that was a sage piece of advice cause when your not playing along you can hear different things pop out at you.
Sorry to be blunt, but it usually boils down to many individual play throughs of the tune,....50 or more is not unreasonable for me at least.
Excellent advice. Especially the listening through the song (while not playing), certain-things-will-pop-out-at-you part. For me, it may be during intense listening through headphones on a flight home, or while driving...that, although I was playing the part in a passable manner (where no one in the band, much less the audience, would notice), I can pick up things that are the icing on the cake...
So, I guess my method would be (not using any notation devices):
1. Listen to the song
2. Listen more, while tapping out the essentials on the floor (feet) and your knees or quietly on the rims (hands), but not actually hitting any drums.
3. Listen more, playing your drum part on the drums
4. Listen even more, without playing, to pick up the subleties
5. Add these subleties to your performance
6. Repeat steps 1-5 as much as possible
I have the luxury of doing my song-learning on a good e-kit, where I can carefully balance the volume of the drums and the track (at non earsplitting levels)...but still...listening critically when you're NOT playing can reveal hidden gems!