Start by using a dynamic microphone on each conga drum. Dynamic microphones are popular with percussion instruments because of their ability to isolate unwanted sound from other instruments in the room. Some common dynamic instrument microphones include the Shure SM57, Shure SM58 and Sennheiser MD421. Place each dynamic microphone in a boom microphone stand. Place each microphone 2 to 4 inches above each drum head at a 45-degree angle.
Use a small diaphragm condenser microphone if you are not worried about noise bleed from other instruments, or if you're not recording in a live situation. Place each microphone in a boom stand, and at a 45-degree angle about 2 feet above each drum head. Some popular small diaphragm microphones include the Neumann KM 184, or any Audio Technica AT4000-series microphones. This same technique applies to most any condenser microphone.
Angle a dynamic microphone into the bottom opening of the conga for a thicker, more "bassy" sound. For the best results, angle the microphone at 45- to 90-degree angle at about 2 to 5 inches from the drum's opening.