In general terms there are two ways to structure a factoring deal. The first is to deduct the factoring fee as a discount rate where the charge for financing is a set amount deducted from the reserve account once the invoice has been paid.
The second method is a funds in use rate which charges a nominal 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 all instances be aware of additional expenses like origination, audits, etc that should be factored into the all in cost of funds.