TET,
it is usual to have a separate project for each top level VI, including dynamic VIs. After, you can create a group including all VI projects.
It can become a mess when you work on several applications projects (not VI SCC projects)under the same SCC repository. In this situation, have a labview.ini file for each project to set a different default directory for each project (use the project directory) SCC stores its settings in the current default directory so it is easy to swap SCC settings just by starting LabVIEW with the project labview.ini file. You set the labview.ini file by creating a shorcut to LabVIEW and adding
-pref "path\to\labview.ini" on the command line.