Hello Cindy,
First, set up an Other Charge item called 3% CC fee, you put the correct wording in the description, link it to either the Cost of Goods Sold account. Then on your invoice add the 3% item in the last line and in the price field you hit the + bar, which turns any numeric field into a calculator with ribbon, and multiply the total after tax by .03 and hit enter. You will have to delete any numbers more than 2 digits after the decimal.
Unfortunately you can't automate the calculation on invoices which charge sales tax because the sales tax shows below the item fields.
