Close-micing an instrument simply means the microphone is close to the source being recorded. Close-micing provides a focused sound and removes much of the natural tone of the room you are in through proximity. Close-micing provides quite a bit more detail; for example, fingers hitting a bongo than distant-micing does. However, if you have a loud sound source, you may not be able to record the instrument at such a close range due to distortion. Dynamic microphones work best for close-micing instruments because they are generally built to handle higher volumes than ribbon or condenser microphones.
Distant-micing techniques require that you move a microphone, normally a condenser microphone, at least 3 feet from the source being recorded. Distant-micing techniques provide a natural, complete sound. If you are recording in a room that contributes to the sound of the instrument, a concert hall for example, distant-micing can be used to great effect for natural reverberation and to make the listener feel as though the music was created in a real space by real musicians. Simply put, distant-micing techniques allow us to hear music the way we normally hear it through our ears---from a distance greater than a foot or two.
Combining close-micing and distant-micing techniques can help you capture a sound both focused and natural. In most professional studios, pianos, trap drum sets and conga and bongo drums are often recorded by blending close microphones and distant microphones together.
Using effects while recording percussion instruments can help players feel more natural and make the recordings sound more vibrant. Simulated room sounds, reverbs, and time-based delays are commonly used to make all types of percussion instruments sit well in a final mix and to help guide the overall feel of the rest of the track. Effects can be applied after the initial tracking process is completed, but many engineers believe that printing effects---recording effects that cannot be removed in the mixing process---make percussion tracks sound more authentic, especially when using close-micing techniques.