The main concern with percussion instruments is the extreme transients they produce. Tambourines and shakers all have extreme transients so beware of getting tambourines too close to a mike and make sure you meter the peak content in the signal.
Congas are usually miked with one mike between each conga thus:
The under mikes are an option that can add depth and body to the sound of congas. Like undermiking toms the mikes must be phase reversed relative to the overhead mikes.
Bongos are similar to the congas:
Here once again watch the transients. You can put one mike per drum if you want to spread the stereo sound for effect and you can also mike them from underneath of you want separation in a studio situation.
Tambourines, Shakers, Maracas , Bell Tree etc.
Tambourines, shakers etc. produce extreme transients so use a mike capable of handling high Sound Pressure Levels if you want to close mike them. For shakers and tambourines I like to have the player stand 3 - 4 feet from the mike so some of the room ambience creates a space around them.
Vibes and Marimbas can be either stereo miked or single miked. A single mike need to be higher than stereo miking to capture the full range of the notes.
The Main thing with percussion is WATCH THE TRANSIENTS