We have developed a system that uses a single code base, consisting of four Visual Studio projects with an admin website, and customer facing website (each system has its own MS
I am not sure I understand your situation correctly, but you can find clues on how to maintain the SVN repository in the Subversion book, under chapter 4.
It seems you either have to establish good routines for the SVN tree, or you have to change the code so that as much as possible is common to all the web sites, with the differences being configurable. For instance, you might be able to create a main project with site-agnostic code, and then code the changes as projects that build on top of it.
As for updating the sites themselves, this must either be done by synchronizing with the appropriate points in the subversion tree, or you have to perform a new release (or upgrade).