IMO the heads are the primary focus - in particular with bongos and congas. Normally you are looking for the high end sound (attack of the head) to cut through a mix - as such you want to mic the heads
I have on occasion placed a secondary mic on the bottom of a Tumba (and in particular on a Djembe) - since the low end of these drums is as important as high end on these drums - I then blend in the amount of low end I need.
Naturally there are several good mics, and many specific for drums/percussion - but for me, one SM57 between the heads (on bongos or congas). If I need the bottom end I normally use a 57 on the bottom as well.
Some people like to mic each head seperate (2 mics on the congas etc.). If you have the channels more power to ya, but I feel the more sends, the more noise, the more potential for problems and more faders to tweak.
