What I mean by "configure" is you would need to custom code skinswap to do such. This isn't a out-of-box feature, as It was more convient to swap all files vs selecting certain and configuring for such.
Yes, skinswap can use the &partner= variable to create different skins for different affiliates.
example:
skin1/
partner1/
partner2/
using &partner=partner2 would use the partner2/ subdirectory for the skin .tpl's. Take a look at the readme.txt for details on how it works.
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