Our shelter doesn't have facilities to house FIV+ or FeLV+ cats (we're in cat overload already), and they're euthanized on intake, unless we have someone who's expressed interest in taking in such a cat (I wish we had enough room for an FIV program, though). But transmission of those diseases is difficult enough so that it doesn't concern me to work in the isolation unit with cats of unknown status. I worry more about things like distemper and ringworm. In any case, we come in through the cellar after working at the shelter, undress, put our shelter clothes in a hot wash, come upstairs, put on fresh clothes, and either shower or do a scrub to the elbows with Hibeclens followed by an alcohol-based hand sanitizer before we greet the cat. That was my vet's suggestion because I was paranoid about bringing diseases home. Also, our "shelter shoes" live in my car trunk and never come in the house...at the very least, do a good bleach dip on your shoes before entering the house, but better yet, buy a pair of cheap sneakers and just keep them out of the house completely. Then, if something happens (like a distemper outbreak), you'll know that you didn't inadvertantly bring it home on your shoes before the outbreak became evident. If I had to pick one piece of advice, it would be "keep your shelter shoes out of the house at all costs."
Also, if you have small hands, buy yourself a box of latex exam gloves, because for some reason, people always donate these enormous gloves that fall off my smaller hands...I spend more time fiddling with the gloves than I do working, so I just bring my own now. Also, if the shelter doesn't have hand sanitizer dispensers, keep a bottle of it in your purse and sanitize your hands between working with cats. It's usually not an issue for me because I have my hands in a bleach bucket between cats during morning cleaning, but if you're brushing and patting cats, it's a good idea to sanitize between cats. If I notice anything abnormal during cleaning (funny stool, worm segments, or non-hairball vomit), I'll change into a new pair of gloves before moving to the next cage, bleach or no bleach.