I am using Atahualpa 3.5.3 with WordPress 3.0.

I would like to create a couple of custom menus as widgets and add to my left side bar. I created one and added to the left sidebar... But, this widget (custom menu) over-rides what I had on top page menu bar. I would like the top menu bar to stay the way I had it, and be able to use custom menu I created for the sidebar only. How can I do this?

You could try createing two menus and use one int the widget. Give them different names. If that doesn't work, you'll need to look for a different plugin