We add a line item to our quotes/invoices for the 2ish% surcharge (manually calculate it then enter it onto that line item). During our quoting process this line item is explained to our customers and sometimes they'll decide up front that they're paying with checks. Otherwise the description explains if they pay online the surcharge is due but it can be avoided by paying with cash/checks. Most of the times our customers will mail a check in for the total less the surcharge, in which case we edit the invoice to remove the surcharge then process their payment. Other times, customers will tell us they'll pay with check and ask us to resend the invoice excluding that charge.
