Same happened to me. I had my embroidery machine for a couple of month and did nothing. What made the trick was going to a class at the dealer. Best advise is to take notes. Just take detailed notes even thought you might think you "got it". Step by step, like: open the file, right click, click open, enter... etc.
Then go home and do it again. You will have time to innovate later, once you feel comfortable with the task/function you learned. My first embroideries were from the built in designs on my machine because I didn't have a clue as to how "take" them from the computer to the machine.
As for the organization, I am trying, I am creating files for each type but I read the comment about the company where it was bought and made me think. I haven't done that but usually they send you and email and I kept the emails in a folder so I guess I could retrieve it from there.
good luck and show us your work.
andrea