My structure for TFS is such:
{Main TFS Project}
3rd Party Assemblies
Development
Source
Integration
Source
I am using continuous integration for my development build, but currently I have to setup the working folder so that I am pointing to: {Main TFS Project} root folder. This is not ideal, because any check-in to the system kicks off my Development continuous build. I don’t want to have the 3rd party assemblies in each branch, because they are shared throughout projects. What are other users doing?
Update
Before I wrote this message I had tried what kroonwijk had suggested, but my build still fails. this is what my work folders section looks like:

In the build definition, you have the ability to specify multiple folders to be downloaded to the build system when the build starts. From http://msdn.microsoft.com/en-us/library/hh190721.aspx:
So just specify your 3rd Party Assemblies folder together with the Subproject folder you want to build in the Workspaces tab of your build definition, and only those folders will be checked and build.