The BBManager will see your data as long as it’s visible somewhere in your computer - on an SD card in a card slot slot, a USB drive, an extra internal hard drive, an external hard drive etc., independent of where the manager software is installed in your computer. If you open a project from one of those other locations, the BBManager will ask you if you want it to remember that location for future synchronization.
The one difficulty with using a USB slot or card slot is that the computer may not assign the same drive letter every time so the BBManager won’t always find it on its own. You should be fine with a permanent internal hard drive or non-changing external drive.
In the event the BBManager can’t find your files on its own, it will simply ask you to direct it to the location you want.