Tuning drums is a bit of an art. Try this and see if it helps you.
1) Low drums are harder to tune so start at the floor tom and work up.
2) Loosen the top head on the floor tom. Tighten the bolts directly across from each other finger tight (one bolt with your left hand; bolt straight across in your right hand). Move around the drum until they all finger tight.
3) Do the same on the bottom head.
4) Now turn each lug a half turn on the top and bottom head. If it's flappy sounding, turn them all an eighth turn more. Repeat until the flap is gone.
Once you get a tone you like, and each drum will be different in each room, move to the mid tom and then the high tom.
5) Use the same process to tune the drums in thirds or fourths from each other. I often tune the toms and snare so they play an arpeggio (toms in thirds with snare a fourth above the high tom). The low tom note can be any pitch. You want the drums to be within their sweet spot. Whether that's C, D, or whatever in between doesn't matter.
If this is something you'll need to do often, I recommend getting the DTS system for your toms. Your drums then tune like timpani and anyone can tune them. You then turn a single tuner to tighten the head much like a guitar tuner works to raise and lower the pitch of the string. The head stays in tune with itself. Kind of spendy but the system does work well.
http://www.drumtech.com/dts.html
http://www.youtube.com/watch?v=zvp_lTzv6gU
Hope it helps.