Best practices for defining files to get for building a VB.NET project

Quick background- we are an Application Service Provider.  Our “applications” are web based with a MS SQL Server backend, but there are literally hundreds (if not thousands) of supporting applications (dlls, exes, services). So the code that gets moved can be VB6 (COM+), VB.NET, SQL scripts, ASP.NET, classic ASP and the like. 

We have been using Finalbuilder for our automated deployments for several years. We are now beginning to develop the process to use it for automating builds of all our component pieces.
 
My question is, what are some “best practices” for handling the compilation of binaries, when running automated builds. Let me give an example.
 
Say I have a simple VB.NET dll with a .vbp and 3 cls files. Say I only modified one of the cls files. I know that I can trigger FinalBuilder server to execute a build on check-in, but how do I specify which vbp project to grab to do the build? How do I know what version of the file to use? Of all the files?
 
I have ideas on how to do this, but I am looking for advice from people who have this figured out already.
 
Thanks in advance.
 
Owen

No one is doing this?