Jim,
1) Buy Professional Community Server Themes. It is a little old but ~90% of it is just as applicable in CS 2008.5 as it was for cS 2007. You can get it from the "bargain bin" at Amazon for 1 cent - can't go wrong at that price.
2) Everything UI in CS is built on the Chameleon engine. Chameleon is a set of server controls much like the built-in ASP.NET server controls but they are context sensitive to what application (blogs, forums, etc.) they are in. Read through the introduction to the controls here. The nitty gritty details about the controls and API is here.
3) Most all of the files you would ever want to modify are in the Themes\[Name of theme] folder (Hawaii if you are using 2008.5 out of the box). There master pages in the Common folder. I'd also recommend browsing through the help articles here to get a feel for how things are modified and how the controls work.
4) Follow these guidelines:
--Start with a set of visual prototypes
--Copy an existing Community Server theme
Copy the Hawaii theme (Web\Themes\hawaii) and create a new folder with all of the same files
--Work from the outside in
Start with the main Master.master file and Common.css files. Tweak the main layout, content place holders, and styles before working on individual content pages.
--Divide work by application
Each application (blog, forum, media, hub, wiki) is contained in its own folder and has its own stylesheet. Theme development work can be divided by application, then, without having multiple developers working in the same files or editing the same style rules.
Any pages that will not be supported by a new theme should be physically deleted. Any missing functionality (integration with an existing application or comletely new functionality can be marked with place holders "TODO: Add X Here")
--Add functionality
Implement all of the missing functionality and replace the place holders with the completed controls/markup/scripts/etc.
--Clean up CSS and images
This is somewhat optional, but there are bound to be some style rules and images that are no longer being used after a theme is heavily customized. Once the theme is complete, the CSS can be reviewed and unused style rules can be removed. Similarly, unreferenced images can be removed as well.