Amazon has free shipping with orders of certain items if it's over $35. Books bought directly through the website usually qualify towards free shipping but if we use credits to buy them at Amazon do these discounted books still count toward free shipping? 

thanks

I think you might be confusing two things together. You can purchase books from Amazon, using PBS as a starting point, but you would be using real money to purchase them directly from Amazon. PBS gets a small percentage as a kickback for the referral, and thats the only involvement from PBS. You may or may not get free shipping based on Amazonsvrules.  The second thing is that you can purchase books from PBS, and in that case, they do let you use credits for full or partial payment of the books, but the books are shipped by PBS and have nothing to do with Amazon at all.

You can't use PBS credits to buy books from Amazon.  You can use them towards buying books from the PBS market. If you use the Buy New From Amazon button that just takes you to the book's page and PBS gets a commission from Amazon but you can't use PBS credits towards the book purchase.