I've been scrapping digitally since February and you're right, you get a lot of stuff, really fast.
I put each kit into a folder titled using the same name as the designer named the kit (keeps me from buying repeats a little).
Inside the folders, I have sub folders for paper, elements, alphas and what every other group (borders and fairs) the kit has.
This past weekend I started to put all my Tennis kits into a "tennis" folder, my scout kits into a "Scout" folder and so forth. I've got a long way to go on that but it has been helping me in my more often used kits (right now Tennis and scouting".
I try really hard to keep all of a kit together.
My system isn't perfect but it works for me so far.
I will say this, I keep my digital kits off my computer hard drive. They are on an External drive. But I also keep DVD's of the zip files so if my EHD goes I don't loose everything. That has happened to me before.