Skunks and dogs don't mix. In fact, skunks and just about any animal don't mix, but dogs simply don't know what they're in for when they approach these odorous intruders. If your dog sees a skunk, you'll need to restrain her and get her indoors, which is relatively simple. The real test is to make sure that your dog never sees a skunk in the first place by keeping them away from your yard.
Keep your dog on a leash when she is outside. If you allow her to play outside unsupervised -- in a fenced-in yard, for example -- she is free to go after any animals that cross her path. In the case of a skunk, this will only result in a foul-smelling pooch. If you're concerned about skunk interactions, keep her restrained when you're outside.
Feed her inside. If you feed her outside, remove the food when she is done, as it may attract skunks. If you two see a skunk when you're outside, keep your dog restrained on her leash and get her inside -- if the skunk feels threatened, its liable to spray both of you.
Remove anything from the property that may attract a skunk, like open garbage containers. Skunks may even come to your yard looking for grubs in the grass, which surface when the soil is saturated -- avoid overwatering the lawn to keep these insects away from the open air.
Spray the borders of your yard with a commercial skunk repellent. Make sure that you use something formulated specifically for skunks, though, and not a generic deterrent like ones made with hot peppers. These chemicals are harmful both for skunks and for animals like your own dog. Following the spray's instructions, spray also any areas where skunks may like to hide, like crawlspaces under the porch.