How do I add % fee and a flat fee for vendors?

I'm sorry if this is not categorized in the right area.

I believe I am trying to set up a multisite. The payment bit is what is throwing me off ( haha, well a lot is throwing me off, but this is where i'm currently stuck).

Ok, so every item is going to be globally accessible from one site - not a bunch of personal storefronts (if I could somehow turn off this function that would be great!). What we're doing is collecting a percentage and a dollar amount. A set denomination from every sale is going to a specific charity. I know how to do the percentage and as far as I know I can only do that through paypal (please correct me if I'm wrong). Is there anyway to do this?