It is not necessary to completely discharge your batteries every time you fly. Just fly until the plane won't fly anymore, or until you want to land, then let the batteries cool before charging them. Completely discharging the batteries every time only serves to waste their useful life.

The most common advice I've heard about storing NiMH batteries is to put them away fully charged. They have a high rate of self-discharge, and you don't want them to completely discharge.