My system is pretty similar. I have a Scrapbook folder and in that folder I have store kits. Inside the store kits, I label each folder store, designer, kit name and then in each folder I label each element by adding a color and whatever it is. Then when I'm doing challenges, I just go to the store kit and search by color. Most of my layouts are a mix of kits as a result, but I like it that way.
Once my kit folders are labeled, I copy them to an external hard drive. On my external hard drive I have the same Scrapbook - store folders. I also have a BACK UP folder where I put new kits. I take those to my desktop computer and drag them into the store folders I have there and then drag them out of my BACK UP folder into the store folders on the external hard drive.
I've got all my kits in three different places in case I ever have a catastrophic failure on one of them. Typing it up, it sounds like a lot of work, but it's not (other than labeling each element in the kits) and it works for me.