We house FIV+ cats the same as FIV- cats. If they get along with other cats, they can go into community cat rooms if there's space, otherwise they have to stay in cages, but there's no special area for them. We do have a "Positively Purrfect" program where we discount the adoption fee to $50.00 to help find them homes. It helps people take notice and ask about the cat and FIV, giving us an opportunity to educate the public.
Unfortunately, we do not keep FeLV+ cats. When we're able to find rescue for them we send them out. Rarely, we have people looking specifically for FeLV+ cats and are able to place them that way, but aside from that, sadly, they are euthanized. Thankfully we have a very low occurrence of FeLV.
We don't see FIP much at all. I can remember two cases in the nearly 15 years I've been with our shelter. Both of them were kittens who stayed in foster until they were no longer comfortable and were euthanized. We had one false case of FIP, and I took him home to foster until he was ready to pass. Turns out the little monster was just fat. He's still a round football of a cat, three years later, lol.