For NDS I used Bulk File Renamer to edit out the numbers in the folders and then during import I used the use folder name checkbox in the import wizard.
Okay I'm going to assume that you didn't move your ROMs into the LB games folder which is the default path that LB scans when looking for the added media so you will have to go to manage platforms choose your system and click edit once in the next form go to the folders tab and change the game path to the one that you are actually using and then try to rescan again and see if you get different results from before.
In the side bar (left hand side) switch the category from All to that platforms and it will show a list of platforms that you have set up once you click one of them it should only show the games for that platform.