Congrats on getting PSE11!! You will love it!
As for organizing, I have found that since I have several designers who sell at more than shop, it is better to organized the kits by<designer name_kit name> than by the shop where I got it. I keep an up-to-date list from each shop showing which designers sell there. Makes it easy to do a quick check if that designer sells at a particular forum/shop when I do the challenges. I do a check about once a month to see if there is any changes at each shop.
I do not break up my kits by papers, elements, etc as I like to work with a complete kit and not have to go searching for what belongs in each kit.
BTW, I love the designers who label each piece with kit-name/initials plus what the item is so that a search with the compter will bring them up.
Have a great time with your new software.