there are not rules except that you hsould get the drums to sound as good as they can before you put up any mics. if youre going to eq then some 5k on the toms and 200 or 250 on the bottom works good. if you need more meat from the snre then 800 is a good one to boost and if you need more snares then like 6k is good.

I can get all my drums to sound good besides my floor tom, whenever i kick the kick drum i get this resonant sound. And i can never really get a good recorded sound out of it but its a great drum. I am just inexperienced.

A trick the current drummer for Godsmack uses (and I'm sure this has been done before, but he's the first person I saw mention it) was to put cotton balls in the floor tom. It may take some experimenting on how many to use. Just let them sit on the bottom head and they will allow the head to resonate from the hitting the drum, but will then muffle the head. How much it muffles depends on how many you use.

Hope that helps.
-Jerry

Holy cow! Thats an amazing tip! Although I sometimes like that resonant thing coming off the floor tom. ...
I was recently thinking of something similar by putting an o-ring (or zero-ring?) resting inside on top of the bottom head. But I'll bet the cotton balls would bounce off the bottom head, but stay in place and tame the symathetic vibrations, and keep a more natural sound.
Super cool.

Beside that, a quik thing would be to tape some Kleenex to the bottom head.

learn how to tune your drums properly first, and recording will be much easier. what mics are you using and what placement etc...