I have just created a virtual directory and placed my app's files into it ready to allow some users to test.
The problem is when I then go to my visual studio project (which uses a different virtual directory when running and seperate code location) I get debug errors randomly appearing from my users actions.
How do I isolate debugging just to the current running project in visual studio?
Since you are running IIS 5.1 you may need to use the Visual Studio Development Server (aka Cassini) to host your Visual Studio Project. This will isolate your project into a separate process from what IIS uses (on Windows XP, IIS 5.1 uses "aspnet_wp.exe")
The default for new Web Application project types in Visual Studio is to use Cassini. If for some reason you need to check or change it, open your project settings and verify it looks like this:
