I use a pump mounted on the side of my tank stand. I just hook up two hoses, one from the pump to the tank, and one to the sink. On the hose end I put in the tank, I wrap a fluval sponge over the end and secure it with a rubber band. This keeps it from sucking in anything it shouldn't. When I initially set my tank up, I removed 5, 10, 15, 20, and 25 gallons of water after the tank was full (measured using a 5 gallon bucket), and applied level labels to the side of the tank.
For water changes, I just pump water out to the level line (I always use the 15 gallon one).
The tank is a 42 gallon hexagon.