Adding a Javascript popup text window

I would like to add a few javascript pop-up windows to the sidebar to display some small html files in a popup window. I'm able to add the href= call to the sidebar.tpl, but when I attempt to add the script to the header in the theme.tpl, I get an error - I guess the application tries to parse the <-- script ... --> statement.

I spent a few hours looking around the application trying to figure out where to put the window popup function so that it gets into the header on the rendered page. No clue. Any advice?

Scott Higgins