If you want to develop a solution / project template in Visual Studio, you have the risk of destroying your entire BizTalk environment. To prevent from destroying Visual Studio, first start a sandboxed instance. Do this by modifying the properties of the start project of your template solution in sandbox mode. On the debug tab of your project properties:
Start External Program ipv Start Project. Specify Visual Studio as the program to start, i.e. \Common7\IDE\devenv.exe
Next specify the following commandline arguments as start options: /RootSuffix Exp
Now you can add a new solution using the template to be debugged via the sandboxed Visual Studio instance.
Think * Share * Integrate 