I have waterfall and small bog on my koi pond, stream emptying into goldfish pond and large bog in goldfish pond. All of my pumps are submersible. There are pumps in skimmers, too. What I have found works best for me is to pull the pumps from the skimmer in the late fall/early winter, before any freezing goes on, and I then attach them to a milk crate and drop that crate down in the ponds. That way the pump is NEVER on the bottom of the pond (just in case any break in line so water doesn't empty to the bottom of the pond in a disaster!), and keep those pumps running. The only thing I shut off is the waterfall, because I feel it does more cooling of the water than anything. I leave both bogs running, and the stream. I have had to raise the edges of the stream to keep any ice from forming and directing the water over the edge, but that was the only learning experience with ice. The other thing was moving the skimmer pumps, as sometimes the water would freeze below where the skimmer could pull from. I'm in south/central IL, so not as cold as northern IL/Chicago area, but we still get cold and my ponds freeze. I don't move any of my plants. The only ones that come in are elephant ear bulbs (they come in dry, stored dry and not in pots). The rest of my plants are hardy, wasn't able to keep tropical lily alive inside, so didn't get any more of them.
Jeannie, if you prefer to use pots for lilies (I think most recommend that they be in clay, not bare root - Addy jump in on this, since I think you did a comparison, and bare root did not perform nearly as well ...), use pure clay kitty litter. It's getting harder and harder to find, since everyone wants the clumping type of litter (me included!!!), but Wal-Mart by me has it still. All of my bog plants are direct planted into the pea gravel, no pots, no dirt of any type. Marginals simply means those plants will grow on the "margin" of the pond, in shallow water. Some of those want to have the crown above the water's edge, some 1-6" below, so it all depends on the plant itself.
Good luck!!!