I do it much the same. In each large file I have a word document with the picture, name, size, and where I found the designs. So a file labeled "Alphabets" would have a word document in it named "Alphabets" and many files in it with the designs. There is software to organize your files which I have not invested in. I would suggest you get it now if you want it. I have so many designs that transferring all of them to new software would be a large chore at this point.
Be sure to invest in an external hard drive to save your files. If your computer crashes you will be very sad to lose so many designs.

About renaming: I'm torn on this one. If I rename a design labeled "djk3" for example, and name it "cat" it may be easier to find but if I want to check to see if I already have that particular cat I won't be able to find it. Sometimes I add to an existing name, "djk3-cat" so I can still find it but then I'm still stuck on whether to put cat in the front(so I see all the cats together) or the back (so I can find the design when searching from a site to see if I already have it).