Admin>Links>Add Link vs Editing the sidebar.php

Hello,

My issues is, in my blog I have a few catagories that I added via the Admin>Links>Link Catagories.

I also use phpAdsnew, so I added a banner rotation script via editing the side bar.php (becasue i don’t see how I can add long javascript in the Admin>Links>Link Catagories)

The catagories added in the sidebar.php appear high up in the side bar & the catagories added in the Admin>Links>Link Catagories appear at the bottom.

I need to add another javascript to the sidebar but I want it to be all the way at the bottom, how do I accomplish this?

Any Help Is Appreciated
Fess