I've investigated further and discovered I have been confusing Web Site projects with Web Application projects. This is what I have found:
Web Application Projects
- Contains Assembly Information via Application Properites (Hidden AssemblyInfo file)
- Creates a working website after compilation
Web Site Projects
- Can contain Assembly Information via an AssemblyInfo file in the App_Code folder
- Creates a working website in situ
Web Application Projects
- Copy the AssemblyInfo file from a Web Application Project only (I tested this)
CrusieControl.NET - SVNLabeller
- Can only overwrite the Version Number in the AssemblyInfo file in the Web Application Project
Thus I shall be using Web Application Projects in the future. Previously I've used Web Site Projects as they worked in situ and we used to just copy them to the Live Server (I know this is bad - which is why I'm asking all these questions as I attempt to improve our development environment).
This answer is my note from researching further which I think is the purpose of Stack Overflow. If someone wants to change the question to something more appropriate to my answer I'll understand - I will attempt to re-tag myself.
Also if I've missed the mark with my explanation here please tell me!
Cheers
EDIT
After further research it appears that there are problems with Web Deployment Projects and Web Application Projects when merging assemblies. The only way to get it work is to name the assemblies differently, which leaves me with 1 assembly with version information and 1 assembly with my manifest information (keeping in mind my version information comes from SVNLabeller). This isn't what I want. So I'm now reverting to Web Site Projects and have discovered I can manually edit the .wdproj file to add extra Assembly Information, it's a shame I can't do it via Visual Studio but is the best solution I can come up with for now.