If you got one of the typical aquarium RO/DI set ups (like Kent, spectrapure, etc) then I think what you're wanting to do is fine. Most people just hook up the filter when needed, collect water in a bucket or tub, then use it for make up and/or water changes.

Working pressure is how much pressure you're putting on the membrane, basically determined by how much pressure comes out of your pipes. A plumber once told me that in a good case, (lots of pressure) that's 40lbs/in2. Much more than that causes a lot of leaks in typical house plumbing. I think most filters are rated to handle a lot more pressure than that. The basic issue is that your filter will put out more water if you have high pressure. I've really noticed this in my new place. As far as rust/iron/sediment, your filter must have some sort of a prefilter; usually it looks like a ball of string in one of the canisters. That's what its for, but if you have old pipes, you can help things out by running the water for a few minutes before hooking up the pump each time. Bacteria is (hopefully) a non-issue on this side of the border, and I'm sure the filter folks' lawyers have something to do with that bit being in the manual.

Matt