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Allright, 20 days later....
Thanks to NobuNobu the developer of the WordPress XOOPS Module, I have found the answer. I thought I'd share it with you guys incase someone has the same problem.
In order to make changes to the index you can't just change the default /modules/wordpress/themes/default/index-template.php. You'll have to create a new directory in that same themes directory with the same name as your XOOPS theme (don't delete the default one). Then just copy the files you want to change (in this case index-template.php) from the default dir to the new theme dir you just created.
Edit index-template.php (in your new theme's dir) and add outside of the post loop (usually at the bottom). If you enter it within the post loop it'll keep repeating itself after every post, so make sure its outside the post loop.
Double check to see if you have your wordpress set to "post paged" in its options and it should work fine.
Again, all credits to NobuNobu for helping me out.