You have an interesting question.
But let me get some terminology correct first to make sure i understand what you asking for.
Any of the following incorrect? (I am assuming this is what you want):
1. You want to have a portal site where merchants (sellers) sell their stuff on your website.
2. You want to process the payment for goods sold on your website.
3. You want to take a % out and then send the remaining amount to the merchant.
If (2) above is what you want to do, then you have to have a merchant account of your own that allows third party processing. Very few companies allow this because you are really wanting to be a PayPal (small sector of merchants of course) but essentially that is what you want.
When you process credit cards on behalf of a merchant or seller then you own the property (the customer information and customer risk associated to the merchant processing by the risk department or underwriting department of the acquiring bank facilitating the merchant account on your behalf). This is the main issue that PayPal had when they started. But they had a lot money to back them so they overcame this problem. Many others who tried, did not.
You can get a third-party processing account that allows you to do just that. But you still have issues such as risk factors vs risk mitigation and they may want to own the customer database or in some case relinquish the ownership over to yourself depending on what they think your account is worth and what the risk may be.
2checkout.com , ibill , ccnow , regsoft (for software) , kagi , paymentonline.com and digitalcandle are all ones you can research and speak with to see if you find the best ones for you.