Do Girl Scouts get a percentage of the boxes sold at booths added to their cookie total?

Yes, but the amount of that percentage depends on their troop and the council in which they live. Some girls receive credit for selling the "average" number of boxes sold during the time they are working at the booth, some receive credit for the actual number they personally sell at the booth, some troops arrange for all booth sales to be split into credit share equally among all girls who worked on that day or at booth sales in general, some are given credit based on the number of hours they work, etc.

Also, different councils (there are just over 100 councils in the USA) handle things differently as well. Different councils give girls differing amounts of "credit" for selling, which can include prizes, scholarships, reduced camp fees, credit at the Girl Scout shop in their area, and even actual money for their troop to spend.