I apologize if this question makes no sense but I'm struggling to figure out how SharePoint and TFS interact, so my terminology might be all wrong.

I'm managing a small TFS2010  deployment, a single project collection with 8 projects in it. It's been upgraded from TFS2005 -> TFS2008 -> TFS2010, and brought all the SharePoint site information with it.

What I have ended up with, once everything had settled, is a SharePoint site with (I think) 6 site collections:

    /
    /sites/Project1
    /sites/Project2
    /sites/Project3
    /sites/Project4
    /sites/TeamProjectCollection

The four projects that were created **after** the upgrade to TFS2010 and SharePoint Foundation are all found as sub-sites under /sites/TeamProjectCollection, but the four projects that were migrated in from TFS2005/SharePoint 2.0 are listed as their own site collection. 

This is causing me several headaches:

* I have to manage user accounts/permissions separately, even though 50% of the users have the same permissions across all sites
* I have to go to 5 different places to manage site settings instead of one.
* Some projects show up as tabs on the TeamProjectCollection site and others don't, which annoys me and confuses some users.

Is there a way to take the single top-level site for each of those site collections and make it into a sub-site?