Hello Caderley,
If you have purchased PDFs on Paizo.com and you have your account synced with Fantasy Grounds you receive a discount equal to the cost of the PDF on the Fantasy Grounds data set. If you purchase a Fantasy Grounds data set and do not already have that PDF on your Paizo.com account the PDF will be granted to your account. There is no discount in either direction for physical books though.
You can sync your accounts by going to your My Account page and selecting My Partner Authorizations. You should get a code you can enter on the Fantasy Grounds site.