i think it is wonderful what you are doing! i only hope your neighbors will agree to the adoption! if not at least suggest a larger hutch/cage?
however! if things work out in your and the bunnies' favor- i think what evil_vegan said is very good advice. also- if they are older than 6 months you should feed them timothy based pellets instead of alfalfa. maybe OxBow or something like that.
i also think a cage is a good idea. my bunnies free-roam but sometimes start acting up by chewing carpet and wood panels and stuff. when i round them up and put them in their cages they calm right down, get a bite to eat, take a drink and take a nap or play with their toys. thats why i like having a cage- its like thier own bedroom.
with litter training- i have found that they use it very well as long as i keep little "bunny bathrooms" around. i have one box in each of their cages, one in my bedroom and one in the living room. lining the front of the box with hay helps mine to use them well. they like to nibble while they do their 'business'
plus, they like those large hi-back litter boxes. these have helped mine to train really well. however- they cannot resist a couple little doodles on the bed now and then
liek evil_vegan said, accidents will happen.
oh! and i also have rats
but i have never let my rabbits and rats out to play together. i just dont feel altogether safe about it... i know (as far as my pets go at least) that one or the other would end up getting hurt.
good luck with the bunnies! i'll be hoping your neighbors agree to the adoption!!!