Recently I came across this very usefull serries of posts at cleverworkarounds.com outlining the entire process from making your branding customizations like masterpage changes to deploying them to your portal.
I strongly recommend keeping this as a reference, there are quite few best practices and things that will generaly make your life easier.
Here they go:
Part 1 dealt with the publishing feature, and some general masterpage/CSS concepts and some quirks (core.css and application.master) that have to be worked around.
Part 2 delved into the methods to work around the application.master and core.css issue
Part 3 delved further into the methods to work around the application.master and core.css issue and the option that solved a specific problem for me
Part 4 then changed tack and introduced how to package up your clever branding
Part 5 SharePoint Branding Part 5 – Feature Improvements and Bugs
On a branding side, here is another resource you might find useful .. a branding webcast i recorded not too long ago: http://www.sharemuch.com/?page_id=197
Hope this helps.
