What we always do is first drain our water heater, then fill up the fresh water tank with the bleach mixture. Turn on the water pump until the water heater is filled up, turn on all the facets and run water through until you can smell the bleach. Then let it set for several hours, overnight if possible.
Drain the fresh water tank -- including the water heater. Fill up with fresh water, turn on the water pump to again fill the water heater, and run this fresh water through all the lines again.
If the remaining smell of bleach bothers you, you can put either vinegar or baking soda in the fresh water tank, and run through everything as above, then drain and add more fresh water. Frankly, we've never done this, as the remaining bleach smell -- what little there is -- doesn't bother us.