I've had many fosters that broke with a nasty strain of KC, and my dogs have never come down with it. One got a hint of runny nose once once, but never fully broke with KC as the dog's immune system fought it off.
I agree with Remo re Doxy -- the alternatives haven't worked as well for us, even though doxy is no longer as cheap as it was. I know several very, very sick dogs who've bounced back in 48 hours after starting a Doxy regimen--it's pretty amazing how fast it helps them. They usually have to be on it for 10 days.
KC can go into pneumonia in the blink of an eye -- when they crash, they hit bottom very, very quickly. I thus think it's pretty important to work with your rescue's vet to get them started on antibiotics as soon as they break with KC. Shelter dogs nearly always have compromised immune systems, so they just don't fight off KC as well as healthy, owned dogs.
I also always use a diffuser with eucalyptus essential oil in the room where the dog is, as the eucalytus makes them much more comfortable (just like it does us, when we have a cold). It soothes the cough.
Also, I add a bit of organic, unrefined, hexane-free coconut oil to the foster's diet (and my dogs' too, if there's KC in the house). Here's an article that explains why:
Remedies for Kennel Cough - Whole Dog Journal Article
ETA: Clean up like you would whenever a person has a cold or the flu. Any products that you already use for that purpose will work fine for wiping down surfaces -- diluted bleach water in a spray bottle is my first-choice for ceramic tile floors or crate pans where a sick dog has been snotting, but Lysol, Clorox wipes, or for a more natural option-Method Antibac, etc. would likely all be fine. I also add a little bleach to the laundry when I wash sick foster dog bedding (towels, blankets, etc. from the crate) and wash them frequently, as they get snot-covered very quickly.
Another thing I like to use when sickness is in the house is Aura Cacia's Medieval Mix essential oil blend, in a diffuser. It's likely inspired by YL's Thieves Blend (which is awesome, but very expensive).