I usually do one compartment per change. I use a gravel vac and get a siphon started and vacuum the section after I have removed the pumps, etc. Tonight I cleaned my skimmer and that compartment, it was the nastiest that I have clean. I put the pump in vinegar water and let it run while I cleaned the skimmer.
I also use the gravel vac to clean my sand.
For putting the water back into the tank, I use a pond pump from Lowe's with a piece of tubing attached,it was cheap and it had good head power. I also use this for pumping out water, if I am only doing a simple water change.