One complexity, that kind of depends on how thorough you want to be....
The water heater has it's own mini-tank, usually about 6 gallons. For winterizing, there are "by-pass" valves to shut it off from the rest of the water system. And then it's drain plug is removed and it is drained.
Previous posters have advised leaving the heater bypassed until after you have sanitized/flushed. If you don't, the bleach water fills the heater, and then normal flushing via the faucets takes forever and lots of water to get it all out again.
But, the heater tank is a nice warm place for things to grow - especially the bacteria that can cause the dreaded "sulphur smell" (although other things besides bacteria can cause that, too!).
So you have a choice:
1) Since the heater tank was pretty empty anyway, leave it bypassed, until after sanitization. Will likely be fine.
2) Or if you want to be really sure, open the by-passes before sanitizing. But after an initial first round of flushing (to get the bleach water out of the supply pipes going to the heater), remove the heater plug and drain it. Put the plug back in, and continue flushing. That will take out most of the 6 gal of bleach water in the heater, speeding up the flushing of the whole system.
The bad side of #2? A bit more work, and on some trailers, the plastic heater plug can be hard to remove and put back.
I've found for me, that I then also have to drain the heater anytime the trailer sits for a few weeks between trips, or I have a high probability of getting the "sulphur smell" problem occurring.....but many others do not have that kind of an issue.
2012 Ford F-150 Eco, Max/Max
Jayco 26.5 RLS, Reese Sidewinder