After you submit a survey, you should see a page that has a link to go to your invoice. If you miss that page, you can always go back to your home page, scroll down to your survey listing, and click on the invoice link.
On your invoice page, you should be able to add your shopper fee and any shipping costs. Then, you may click the Add button or the Submit invoice button. I like to do the Add thing first so that I can see the expenses that are added to the invoice. Then, I submit the invoice. It's an extra step but I use it to make sure I didn't make a mistake entering my expenses.