Reg E has not applied to business EFTs since the Reg was written. It is a consumer protection regulation.
The good news is, you have no federal requirements so what do you want your agreement to be? If you offer a branded card, Visa or MasterCard, check their site and see what the terms are that you must offer, and incorporate those into an agreement. I would include them in a Reg E - like agreement as a starting document, but keep only what you want to live with that isn't required by state law or your vendor's terms. Focus on who can use the card, liability, notification requirements, etc.