I am having a little trouble getting a template for a shooting script: Two columns one for audio, one for video, maybe a third for time(code). I downloaded the demo for Final Draft, and it seems to be more of a screenwriting tool. Does anyone else write their shooting scripts this way?

What you're looking for is called an "A.V." script, the term 'shooting script' is a variation on the screenplay form. Also search for "Dual Column A.V." when you are looking for templates. I'm sure Final Draft has that option, though I write with Scriptware. Most of the major screenwriting programs have the option.

I created my scripts using 3 columns as a table in microsoft word.

Otherwise, you might want to try this:
http://www.chicagomediaworks.com/2instructworks/3editing_doc/3docedit_scriptmpl/3editing_docscripttemplate.html