To enable a blanket percentage-based fee for any invoices being paid in the Member Portal "Online Bill Pay" page, go to Admin > Global Settings, and click on Online Payment Settings.
At the bottom of the page, check the box "Enable Credit Card Fees in Member Portal."
Enter the percentage of the invoice total you would like to charge. This percent will be used to calculate the line item amount for the fee, by adding the total of all line items per invoice and multiplying by the percentage as a decimal. To charge a 3% fee, for example, enter "3" and the total will be multiplied by 0.03 to determine the amount.
Select the Revenue Item from your organization's list of items to use for the fee invoice line item.
Once this is enabled, your members will see an asterisk appear next to the amount to pay based on which invoices they've selected, with text at the bottom that indicates they are being charged x% as a credit card fee: