If you are asking how do you enter your 5% fee into your QB, you would enter it like you do any other income. You can either make a monthly invoice in your company to the non-profit for the amount of the 5% fee you earned that month and then receive payment. Or you can simply enter a deposit that lists the non-profit enter the type of income to the income account of your choosing and deposit it to your bank.
Since you say you are a 501c3 acting as a fiscal sponsor for a project, I would check with your accountant in your state to see if that 5% falls under donation revenue or for-profit income revenue.
