You have to make them not want to dig in your pots. The easiest way to solve the problem is to purchase some hardware cloth no larger than 1/2" weave (not chicken wire) and cut it to go around the plants in your containers. They cannot dig through it. There are commercial repellents sold that claim to keep the squirrels at bay, but there are questions about their effectiveness.
After you exclude them with the hardware cloth, consider leaving one undone (with no plant, of course) to give them something to continue working on.
Online Resources:
Tree Squirrel Control
