Correct way to skin a board
 

I'm responsible for a large forum (1.5 million posts) that has been heavily customized. The customizations include templates, CSS and images for buttons and icons. The templates and CSS were modified via the admincp. The images were merely replaced on the filesystem.

This makes upgrading a nightmare. I end up with tons of templates to update and I have yet to get the images directory correct the first time.

I've been asked to setup another forum for a new site. I don't want to repeat mistakes.

What is the right way to skin a board? Is there a way to do this that makes upgrading easier? I have full access to the machine and I'm intimately familiar with source control management systems (This machines uses subversion). If there's documentation on this that I missed in my searching I'd be happy with an RTFM reply.