I have always used Visual Studios built in GUI support for configuring my projects, often using property sheets so that several projects will use a common set.
One o
It sounds like it could be worth checking out a build tool - at my place we use a custom made tool that watches files and projects for changes and figures the dependencies and compile order. Adding a new file is no big deal - compilation is done with msbuild.
If i had to compile more than a bunch of projects I would use something like nant: http://nant.sourceforge.net/