If that does not fit your needs, you can use a different personality (e.g. "mobile").
Start C::B from console or from a batch-file with the "-p" parameter (e.g. "-p mobile").
That will create a "mobile.conf" and maybe other conf-/ini-files from plugins in the default folder (all called "mobile.*").
Move the files in the directory where your mobile executable is, and start it with the same parameter set.
If you do so, it should not conflict with a C::B installation in the default folder on the PC where you use your USB-Stick (or whatever you have).