You can go to a folder and search that folder and its sub folders for rom files and import them easily, just type in *.cue or *.bin or whatever the file extension of the file type you are looking for. You can then use Control + A to select all and drag them into Launchbox, you can also do this using the Tools > Import > Rom Files method as well, I just find the drag and drop method easiest.
I sort my CD based systems like this, with each game in its own sub folder.