I want to use the code: <base target="_blank"> on my 'listed at' page so that when you click on the fanlisting icon it appears in a popup. I have a menu, header and content layout, and when i put the code above on my 'listed at' page but it made it so that even the links in my menu/navbar were popups too, is there a way to make it so that only the links in the content section come as popups?

You can always add target="_blank" to each content section link separately. Or there is this target _self that I've never used but it might make links open in the same window if I got the description right.