I asked this question when I first started using Launchbox and unfortunately it's one of the organization and ease of use features that, IMO, is glaringly missing from LB. It was explained to me that you can go into a text editor (notepad+ makes it easier) and edit the .xml file to change the rom location, which I did. It works, but an obvious PITA. The other option is to delete and start over each time you make a mistake or move something to a new folder. If there is a new way to do it since I originally posted about this I am not aware of it.
Unfortunately, organization features seem to get passed over a lot because it's based on what features people vote for on the bitbucket site.