To keep bugs and critters from fouling the water, make
sure your cistern is covered with a screen. if you meant when I am
using the double pumps, cover the first container as well.

pumps... we may end up going with a 120v pump in the end, although I
was told by the one company I talked to that if I tried to replace the
220 with a 110 I would have to switch the wires to it or they would
overheat. I question his statement a bit though as the wire that is
currently running for the 220 pump is a 12/3. Of course, even if he
was right about it, replacing a wire is a lot cheaper then setting up
220, and easier then carrying a bin and two pumps back and forth.

mold and algae... the only reason you will get either of those is if
you either have a) standing water or b) moist conditions in the
building around the cistern and no air circulation.

Rain Water... yes I could set up a system to divert rain water,
personally, I prefer my water filter through a lot of ground first
thanks. Although we are fairly isolated where we are, there is an
medium sized airport that take offs and landings go right over our
place. They are still fairly high when they go over our place, but
very high is also where the rain comes from. Plus about 50 miles to
the north is a press board plant that pumps shit into the air, even
though they claim it is 99.99% water steam that comes out. How many
times have you seen yellow steam that leaves a dirty yellow powder on
the ground in the town beside it? None of those things are of
immediate effect on us, and in general our air and water are very
clean up here, but I would still rather avoid those possibilities for
the house system.