Oh Groan! The Horror! Keeping the books organized is my own nightmare, as well. Adding to the confusion is the fact that I download books to my work computer, husband's computer, and my own. Read around the threads, use the search box, and you will find a million ways to organize things.
Back in the summer, I took 2 weekends and really got organized. I bought me a brand new flash drive specificially to put books onto for backup. Marked everything either TBR or Finished. It was a beautiful system. I had everything in one place. "You are going to keep this organized from now on.", I told myself.
OK, I ended up with something like 75 books TBR, so I put a moratorium on downloading and started reading, vowing not to download another book until I got caught up. So I got caught up and finished them. Now yesterday, I downloaded and/or bought about 30 books and they are on my EB-1150 and work computer. Flash drive is still sitting at home plugged into husband's computer's USB port. I have to remember to bring it and backup the new stuff.
It's too easy to spend more time downloading and organizing than spend actually reading. All of this is to say that you will have to figure out the best solution for your own situation. There are several threads that discuss ways to organize things online, on your reader, etc.
Be sure to post your solution when you find it. Good Luck!