In your target file you need to update the LibList pbls to reflect the new paths. Example "SUPPLIER\\supplier.pbl" (assuming you put the supplier.pbl in a folder called 'SUPPLIER'.
Don't bother checking in the workspace. When adding the target to the TFS project you can choose to add all objects at the same time. I've done this without any issues (but I didn't have more than a few hundred objects in the project).
Do the check in from PB. Assuming you have the 'require comments upon checkin' option checked, you will be prompted for comments which are brought into TFS. My company uses a ticket tracking plugin into TFS which requires us to also associate a checked in object to a specific ticket but that is not a requirement for a 'vanilla' TFS set up as far as I know.