I ran into this problem with rocketlauncher per-game fades(start up images), because it needs them to be in a folder of the game name. So I exported my images from CTC, used fuzzyrename to get them to be named the same as my rom names, then used a program called "folderit", that will scan a folder and put each file it scans into a folder of the same name. That could be useful here. It was a bit tedious. But it actually ended up not being that bad overall.
Then I ditched the entire thing and went with the Launchbox plugin "custom startup images" instead haha.