Create the RMA as normal and generate the credit memo and then add on the credit memo using positive numbers.  When posted the system will make the amount a negative

Entering the number as a positive added to the amount of credit being given.  I entered the number as a negative, however in the total column it showed as positive subtracting from the total credit due. See below:

I printed the invoice as a PDF and the total is correct, but I have not yet posted the invoice to the customer's account.

Just trying to confirm that I understood you correctly and this is right.

One more question on this subject. 

I also have to deduct some parts that were needed to repair a unit and return it to stock. 

Would I enter those parts as negative after processing the credit (but before posting, so they will be deducted from inventory) as with the fee in my earlier message?