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It's your choice how you want to do it, but if your running multiple affiliate accounts just make sure the links point back with the correct codes and you could have however many you want.
As an example I think my site currently runs with around 10-15 different affiliates, this is changing depending on what projects are going on, there are some niches which will have more in due to new ventures and smaller projects.
If you need a hand putting together some sort of management script or system please just ask
Rob
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