I have the files/designs I've accumulated organized on my computer as separate files - one folder for each design.
I have the colour change sheet and the actual embroidery file that goes to my machine in that folder.
So far, that has worked for me.
When I get a lot of any one type of design, eg, bookmarks, I make a new folder for that title and put the other folders in as subfolders. For specific techniques, I add a qualifier to the name of the folder (i.e. FSL = free standing lace, ITH= in the hoop)
I may find as I get more designs, that I need a format that allows for a small picture of each design to be seen prior to opening the colour change sheet.