In general terms there are two ways to structure a factoring deal. The first one is to deduct the factoring fee as a service charge where the charge for financing is a set amount deducted from the reserve account once the invoice has been paid. The charge can be for the initial 15 or 30 days and then the same rate is pro-rated for additional days while the invoice is outstanding.
The second method is a funds in use rate which charges an administration fee to submit the invoice for financing and an interest rate that accrues while the unpaid invoice is outstanding. The interest rate is usually prime plus a certain amount of points.
Both ultimately get you to an all-in cost of funds. In every instance be aware of additional expenses like origination, audits, etc that should be factored into the all in cost of funds.