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The "rotten egg smell" usually comes from the hoses, not the potable water tank. The most effective way to clean it is to add a hose Y valve to the system (it goes in backwards (see pictures in Hayden's IP Photos.com site) so you can flush out the plumbing without getting the chlorine in the alum tanks. You might also want to rig up a bypass for the hot water tank as once chlorine gets in there you have to do a lot of flushing to get it out.
Top answer your original question, I'd suggest draining both tanks--at least you won't worry about them.