They're basically doors that open on the engine nacelle, to help cool the engine, usually used during slow airspeed and high RPM situations.  To determine whether or not to use the cowl flaps, look at the cyclinder head temperature gauges, and try to keep them in the green arc.

hope that helps

depending on the design, they can also act to keep the snow out... as for example on the I-16, Li-2 and Yak-18T