I was able to find an add on in the QBO apps section called Freedom Merchants. Very affordable, and I will hopefully be able to start using it soon. Haven't started to yet. 

This vendor is an add on that integrates with QB online. It automatically applies the CC fee  the customer pays with a CC and the fees are lower than QB Payments process. It may be the best and most efficient/cost effective way to offer the pay now option to our customers… It is $25.00 a month.

If we use the QB Payments to process the online pay now cc payments then:

1. it is not an automatic process. We will need to manually add the processing/convenience fee to each invoice we send.
2. The calculated 2.9% plus $.25 per transaction would be added to the total fee we calculated so we would be paying fees on our fees so the amount charged to the customer would not cover the actual fee.
3. We would have to deduct the fee if the customer chose to pay by check.

I am looking into work arounds researching the QB Forum and spoke to the QB help people. Their suggested method to collect a convenience fee from the customer:

1. Manually Add the fee as a separate line item on each invoice we send (added fee gets a fee so calculated amount doesn’t cover fee total)
2. Or send a second invoice to the customer for the fee
3. If sending a second invoice for the fee then INSTRUCT them to pay it by check (or we will end up in a cycle of collecting fees for fees)
4. Put note on invoice that tells customers TO DEDUCT the fee amount on invoice IF they intend to pay by check (we would then manually deduct fee once check was received).

They may be the best solution if you want to continue using QB. I haven't found a good alternative Accounting software yet... Thank you!