A bunch of questions - first time user

Hi;

First off I'm new to MSBuild & aspnet_merge - we've used nant up to now. I just created a web deployment project and have a couple of questions. This is with most properties set to the default value.

This creates a bunch of files in portal_deploy\Debug\bin including all the .compiled files. I thought this would have just the created DLL and reference DLLs?
How can I keep the web.config file seperate from the pre-compiled part? I would prefer to have just 2 files, precompile.dll and web.config.
We have a project that builds a DLL and then our website. The DLL project we obfuscate and then sn again. How can we do this as part of the web deployment build?
How do we sign (as in signcode, not strongly name) the final precompiled.dll?

thanks - dave