I Want Sidebars to Load Last

I have my sidebars loading last on my front page. I did this in the index.php file and all is working well.

The problem arises when you click on comments. The sidebars load FIRST when you go into a comment.

Any ideas? Where do I make the change for that? Is that also in the index?

This is my code, if that is the least bit helpful.

Thank you in advance! 🙂

[moderated: Too much code! Please consider using a pastebin service like http://wordpress.pastebin.ca/ instead]