The best way to get rid of the skunks is to deter them from entering your yard. This amounts to removing the food supply (your pet's food and water supply, the garbage, or invertebrates in the lawn) and/or fencing. If you apply grub control, understand that the damage can continue for two weeks. Generally, grub control should be done before the damage begins. Otherwise, the skunks keep eating till the grubs are gone.
If legal, trapping is an option. It is not recommended that untrained homeowners try trapping and moving a skunk. Information on trapping skunks can be found below. Remember that if the habitat is attractive to skunks, it will be attractive to future skunks as well. Make your lawn and yard as unfriendly to skunks as possible, and see what happens.
Resources: (online)
Skunk Control
Skunks
