While I isolate the water heater during winterization and the entire "de-winterization" process (to keep crap out of my pipes); I sanitize the system AFTER I fill the hot water tank.
That way the tank gets a good dose of chlorine.
If you decide to drain after sanitization, be sure to "re-isolate" the water heater so the crud in the bottom of the tank won't get into your pipes.
My technique is to just drain the fresh water tank (only) completely after sanitizing the system and then refill it with house chlorinated water. Then I just run the hot and cold water through the taps till the chlorine smell is gone.
Lou and Laura with Bella - German Short Hair Pointer
2008 GMC Sierra 2500HD Crewcab SB Allison Duramax
2010 Flagstaff 8526RLWS - Superglide 3300
HAM CALLSIGN - KC3FFW