Rob Mensching describes the proper way in this answer.
Alternatively, you could use the following:
The bootstrapper creates logs in your user's temp directory, ex:
C:\Users\[username]\AppData\Local\Temp
Run your boostrapper and attach the debugger to your setup.exe.
Call
Debugger.Launch()
(from the System.Diagnostics namespace) in your code to launch your debugger during runtime.