OK, so I readily concede that I\'m a newbie when it comes to continuous integration.
That being said, I\'m trying to set up a CC.NET environment to educate myself, b
Leave the csproj file well alone (as you say, you don't understand it).
Create your own msbuild proj file and call the csproj (or sln) from your main build file via the msbuild task. Tell your CI server to build your build file.
This seperation makes it easier to add your own pre and post tasks (unit tests, smoke testing SQL scripts, fxcop/other static analysis, etc.) and you won't break your working environment. It also means you can do your custom targets in whatever you wish (msbuild/ant, etc.) Have a look as MSBuildContrib on codeplex for extra goodness.
You don't need visual stuido on your build server (unles you have deployment projects, unless this has also been changed since I last looked)