Okay I sorted out the issue of using OS Affiliate with a templated system, man that was a pain! For those that wasnt an idea of how I did it, I wish i could explain it. It was the hackiest, guess work I have ever done. There was one } that had to be removed from the header.tpl and all the affiliate pages, well I ripped the <left> and <right> boxes out, made a new menu with the links and placed it at the top of the page. That solved the way it fit into the template.
I also updated the icons to be abit more modern, if you want them PM me and I'll post them. Despite all the trouble, I'm happy to have figured it out myself, along with little tips and such here and there regarding my problem from the great ppl here at osc.