Pagination allignment problem.

I made a custom category page for my blog. I took the code from a single post, and put it inside the wordpress loop. This did the trick, but the only problem when I try to add pagination to the bottom of my category, it shows up at the end of the first post. I’ve tried putting pagination code outside the loop, in its own div and I can’t seem to figure it out. Any one have any ideas how I can fix this alignment?