ckosloff is right about the blank sidebox. The Admin Editable sidebox was intended primarily as a way of adding HTML content via the define pages editor. For adding custom content other ways, the blank sidebox offers a cleaner start and more guidance.

There are no incompatibilitioes between Zen Cart and javascript. Indeed Zen Cart uses javascript and has a sophisticated mechanism for loading it. There's a readme file about it int he docs folder that comes with the Zen Cart release package.

Where problems do sometimes occur they appear to be more about issues integrating javascript directly into php code. This is tricky and not an approach that I would recommend. Better to load it using the Zen Cart mechanism provided and mingle only calls to the functions loaded with the other code.