Yes 100%. When you add a system to Launchbox you tell it where that systems roms are stored, then you get three options, "move roms to launchbox folder", "copy roms to launchbox folder", or "leave roms in there current location", so you would just select the third option. Also all the media paths are editable after you have imported a system, so you could move certain things elsewhere and then just edit that location in Launchbox. For example,
Also it is worth mentioning that Launchbox itself is a potable program, so it can be moved around to different folders/drives if so desired, and as long as the roms themselves didnt move it would still work. Also there is a option to change the rom path for systems in Launchbox, so if you moved a system from the USB drive somewhere else, you just need to choose the option in Launchbox to change the rompath for that system and point it at the new location.