Hi there.I have have about 2 years experience in afiliate-commision-based business but have considerable experience in e-commerce and epayment solutions.
This is a very creative concept and believe it has real value. Since your business model border around afiliates COMMISSION then I like to believe also that when you successfully sign up as an afiliate, you receive a unique ID and URL for your afiliate membership.
Trying to achieve this 'solution' of concierge-type checkout might not be the right way. Why? Because you want your customers to have a seemless order fulfilment experience. I do not think it makes a good customer experience for your customer to enter his/her credit card details twice along a payment fulfilment journey.
Your concern as an afiliate should be the afiliate-merchant recognizing the purchase fulfilment referral SOURCE - which is your unique afiliate ID. So, you have the customer click on your website link for checkout , while he/she is redirected to the main merchant's website for payment fulfilment AND your ID parsed during that transaction to your afiliaite-merchant for proper reconciliation purposes. After all, you referred the customer and your entitlement is your COMMISSION.
Another reason why providing a separate 'Checkout' experience might not work is because you do not have control over the PAYMENT PROCESSOR agreement or partnership with your upstream merchant.
The solution you might explore should be: 1. Consult with each afiliate-merchant and discuss on an AUTOMATED method whereby during the checkout REDIRECT process towards the afiliate-merchant CHECKOUT PAGE, your ID will be captured from the URL so that your commission is remitted appropriately in line with your UNIQUE AGREEMENT with each afiliate merchant. 2. You might need to discuss with each of your afiliate-merchant around API(application programming interface) design to help you achieve item 1 solution.