Dreamweaver Templates, Editable Regions and CSS issues

I am working on converting a site from HTML to XHTML, altering all nasty tables into DIVS and CSS.

The original site pages were created using a saved Template page consisting of two columns with a header and footer.
The left column is Nav and the right column is the main content. The main content has the Templates editable region in it.

I kept the Template with the same layout but using DIVS instead of tables.
However I have been spending a lot of time working on cross browser alignment issues and I have discovered that it is the Editable region that is knocking everything out.

Is this a known issue and should I disgard the Template approach?
I cant see any problem doing this as any sitewide changes can be acheived by altering the CSS and using Find&Replace to update links etc to the souce code.
If this is the case, are Templates no longer necessary? Or am I missing something with regards to applying the Editable Region?
Maybe I need to apply CSS to the Editable region somehow?

Any advise welcome. Thankyou

AK

I worked out it was one of the DIVS that was causing a problem not the Editable content region.

However I have an issue with creating a row below 3 columns. I am using relative positioning within the main content DIV.
I set the row to Clear: left but this positions it below the nav on the left, and is not relative to the middle content.

It really just needs working at > END

Well one thing that I have learned to do is use Includes on everything that is the same throughout pages, links, Css code, and all that. This makes there be no need for templates at all and cleans up my code tremendously.