How can I set up my products where customers only pay for the side that they edited on?

To set an extra charge based on the custom design added per product side/panel, go to the Price per size range option. For example, $5 will be charged for added designs on the first side. Another $3 will be charged if customers add designs on the 2nd/other sides.

As you have to set the price based on the size range, the price will be counted based on the design size of that size range. 

Check out the tutorial for more details.