Some networks go so far as to indicate how well each merchant's account is funded, allowing you to choose whether or not you should promote their products. Other networks will suspend or put the merchant's account on hold until such time as they've deposited sufficient funds.
You don't get any of that security when you sign up for a stand-alone program - a program that is administered by the company itself. While you don't need to worry about Amazon or Match.com, it's sometimes hard to be sure about the smaller unknown companies
One way to gain some security in that regard is to find out whether the company uses third-party billing to process their payments and handle affiliate commissions. The third-party processor takes in the money from the customers, and makes sure that the affiliates receive what is due to them. Depending on the affiliate agreement, you may end up splitting the payment processing costs with the merchant.
For example, one of the dating sites that I promote and that uses CCBill for payment processing, offers a 50/50 commission split. That fifty percent turns into 42.5 percent after the 15% CCBill fee is also split.
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