Multi-Site Drupal, theme structuring and Zen theme

Thing I plan to do is to make many websites based on Drupal core.
All of these websites will be quite small, but there will be many of them (in matter of hundreds).
I'm working on this with one HTML / CSS coder, guy who should make themes for every website we make.
He doesn't know much of a PHP (enough for PHPTemplateEngine tho) therefor I what I want is to make as little interaction between me and him as possible. He shouldn't touch PHP part of themes, I shouldn't touch HTML part of themes.
My question is:
Can you tell me what structure of theme folder should I use, what's your opinion of Zen theme for beginning of Drupal theming and how can I make automatic JavaScript and CSS loading script for themes?
Also I'd greatly appreciate any tips concerning multi-site Drupal setup, best practices and so on.
Thanks in advance.

Solution

With regards to drupal theming you have a couple of options:

If all the themes will share 98% of the same code base and just have different classes etc to style it visually different (say a different heading colour), then you can get away with one drupal theme and use theme settings to alter the configuration of the theme on each site. This has the advantage of having to maintain only one code base. Zen can still be used as a base theme if you wish
Another option is one you have mentioned above, in which you have a base theme which declares all inherited code, and sub themes to which override specific parts of the base theme to create the necessary effects. I would suggest that this is the better option if your themes vary wildly from one site to another. There is a administrative burden with this option though, as say you have 100 sites, you could potentially have 100 sub-themes to maintain and provide fixes for.