Organizing Books on Apps

Okay, as I was writing last Thursday's blog post, I had something pop into my head and decided to write this post right away before I forgot all about it.
How in the world do you organize your eBooks?
I have a major disaster on my hands and literally spend forever trying to find which book to read. I have so many books on multiple reading apps (Kindle/Kobo/Book Funnel/Etc.) and nothing is categorized or organized.
How do I sort things when I've been collecting eBooks for years and haven't organized anything? How do I even start to sort out this mess?
The other night, I had some free time, and I wanted to read a book. I knew I had just downloaded a couple that were intriguing, and I'd been excited to read. Then I went into the app, and I didn't know which ones they were. I kept opening book descriptions and reading them, but I never found any of the stories I was looking for.
I'm sure everyone else must have a system in place. It must be only me with this chaos.