Sanitizing cleans the whole freshwater system. Even if you don't use the freshwater tank, you should sanitize it anyway. You just don't know when you might use it. The by-pass for winterizing is just to isolate the water heater so you don't have to pump 6 to 10 gallons of anti-freeze in it. Look in the library (tab located above) for sanitizing procedures (and a lot of other good information). When you sanitize, get the chlorinated water in every part of the system. Don't forget the toilet, outside shower, and low point drains. Also put the plug or anode back in the water heater and swap your by-pass valves to sanitize the water heater. I usually swap the valves after I have flushed the anti-freeze out so I don't get any anti-freeze in it. If you have an ice maker and/or a washer hook-up, don't forget to sanitize them also. Any bacteria, bad smells or bad tastes can easily spread from an untreated section of your plumbing, so be sure to get the sanitizing solution in everything.