I have hardly any experience using the "free 50", but I don't think you have to do anything to get them. Any fees you incur - by using non-free "extras", or by listing in a non-free format, or by listing additional items past the free 50 - get added to your eBay invoice.

Before you finally submit an eBay listing, I think you are shown exactly what up-front fees are going to be associated with that listing.