I had a momma skunk decide to give birth under my big coop awhile back. I tried everything to get them to move on. I put a radio on in the coop for noise, I strung lights all around the coop. I tried calling several places to come and get them but nobody wanted to capture them.
They got old enough to start spraying and sprayed my dog twice. Every time I saw them, I would chase them with the water bottle to annoy them to get them to leave. (spraying is the last resort for them, once they spray, it takes awhile to rebuild the fluid to spray again, so they will stomp their feet at you first to scare you) When I saw them out from under my coop, I would take dirt and rocks to fill in the areas they were crawling in and out of, but they always managed to get back under the coop. It took about 4 months of this but they finally left.
Skunks are not great to have running around, hopefully they don't spray your heating or AC unit outside. That happened to a friend of mine and her whole house smelled like skunk!