Hey Kessa, I think you can do something like this:
After clicking "configure popup" for the layer you want to show percentages, you can click ADD under Attribute Expressions. Then just choose the field you want to show with the percentages by clicking it once. This should add it to the script box. Then on the same line you can enter this: + "%"
When I did it to test, it looked like this:
It worked for me so I'm thinking this should do the trick for you.(This was after I clicked test to see if it worked)