How hard are you hitting? The harder the stroke, the more the reso head will be excited and the fundamental pitch, i.e, the pitch of batter head, reso head and the drum itself, will become more clear.
Obviously, tap the batter head lightly and you will only hear the pitch of the batter head.
The relationship between reso and batter had on toms is quite interesting. At least within a reasonable tuning range, a 10" tom for instance, with the batter head tuned Bb and the reso tuned C, will produce a fundamental pitch of D. I often take this in to consideration when tuning, and all my drums have the same pitch interval between the heads so that they will have the same sound characteristics, but different pitch of course. I've found that my 10" tom sounds best at a D#, so I leave tune the reso C and the batter just slightly above B.
I have yet to find a similar relationship with the snare heads, but then I never really bothered with the fundamental pitch of the snare. I do however, always tune the reso around A, and tune up the batter had until I reach what I'm tuning for.