Hi Moon Shadow. I think you are very confused about the operation of a water maker. Flushing the water maker is usually done with the fresh water you have made. Its a simple process, and if the water maker has been installed correctly, can be done by just flipping a valve and with a small bucket for the water you will use to flush. The intake to the unit is just switched from the seawater to the fresh water in the bucket (and preservation chemicals if storing the unit).
I'm not sure which water maker you will use but most operate on 12 volts. Solar, wind, and the engine alternator are used to charge the house batteries. No special "modules" are needed. Solar and wind can not operate the water maker without the house batteries as the current draw will be too high. Depending on the water maker, you will only need to run it for a few hours a day. The rest of the day, the solar is recharging the battery. Its not necessary to carry hundreds of gallons of water, only make and carry a reasonable amount you may need for the next several days. If AC/DC capable, the water maker unit only converts the AC to DC. Some water makers are run with a high pressure pump mounted to the engine.
A`ohe `ulu e loa`a i ka pokole o ka lou.
No breadfruit can be reached when the picking stick is too short.