Being new to CSS with an existing table based site, we are considering using CSS for our basic two column site layout, but stick to the existing tables within the DIVs. Will that be a problem, or should CSS go all the way.
Deciding whether to ditch tables altogether in favour of CSS is very much up to you. Technically, tables should only be used for tabular data - but many people still use them for positioning elements. Doing the same in CSS requires a little more work, but the same result can be achieved - meaning cleaner code, standards compliance and knowing that your code will work in all compliant browsers.
The approach your described will work fine - there is no problem putting tables inside a CSS layout framework.