How to merge a working menu system with Drupal?
I have a perfectly working web site with a menu system on the left side and a banner on the top.
My goal is to use Drupal to add a "Knowledge Base" section to my web site, to take advantage of the CMS and search capabilities of Drupal.
However, I want my Drupal Knowledge Base to look similar to the rest of the existing web site, with the same menu on the left and logo and header on the top. I can put the HTML for the header and menu anywhere, but I'm having a real tough time figuring out how to get it into Drupal. I started with the zen theme, figuring I could make a sub-theme with my menu and header stuff, but I can't figure out where to put it. I haven't seen a similar question in the forums. Perhaps I'm not looking in the right place.
Or is Drupal even the right tool for what I want?

Without more to go on, it's
Without more to go on, it's hard to know what the best solution would be, but some possibilities
- existing menu gets created in straight HTML as a block and the links go to either standard taxonomy pages or to taxonomy pages managed by views
- existing menu gets recreated as a new block and put into your theme as a block wherever you want and styles as you want
- existing menu gets folded into a menu like primary links and shows up wherever the theme puts it.
- you use taxonomy to recreate the existing menu by creating a vocabularly where the hierarchy matches your existing hierarchy and then you use a module like Taxonomy Menu or Advanced Taxonomy Blocks to display a taxonomy menu
Probably more ways that I haven't thought of yet.
Also, if you use a theme like Aquia Marina, Aquia Slate, Waffles, one of the Symphony free themes (see http://drupal.org/node/596022) you'll have a lot more regions to choose from.
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