I'm not sure if who might need this information, but man it's hard to find. Kindles aren't as user-friendly as one would expect.
If you need to move books and documents onto the kindle using your computer or mac (via USB) you need to put the .epub .mobi or .pdf files into the "documents" folder.
The kindle will create a ton of "[book name]_[hash].sdr" folders to match and store metadata like your place in the book.