Actually, I hated the idea at first, but now that I've been working with it, I have to admit that I really like it. One, it makes it easier to fix just the thing needing fixing. And two, I can use multiple headers, sidebars, and other pieces for different categories or ways of doing things without a lot of stress and strain.
The first thing I recommend is that you go through each template file and put a comment code at the top and bottom of each one that identifies what this is. For example:
<!--sidebar file begins-->
blah blah code and tags
<!--sidebar file ends-->
And then go through every DIV and class and identify where it ends with another tag:
<!--sidebar menu ends-->
When you generate a test post, you can view the source and see where everything is as it is now identified. It really helps a lot.
Also, I know you know your stuff, but this is a big change and way of thinking, so take time to go through the WordPress Codex documentation as there are a lot of great articles in there that will help you do much of what you are doing step by step.