Adding affiliate banners to theme

I have started delving into the world of affiliates. On my blog page, tmreisinger.com, I have a three column layout and I am filling up the sidebars, but a new affiliate for me uses banners. I think the best place for me to put the banner is above the posts. would that be part of the header or would I put that in the page template?? I don’t necessarily want it to show up at the top of each post , but just at the top of the post column.

Would it be a good practice to get into putting my affiliates in there own .php folder and then link to them and what would the code be for that??

thanks in advance
Tim