right. these edits are called side car edits. basically it is just an algorithm that allows the computer to backtrack the changes you have made to the RAW file.
The way I organize my files is a little different than most because my priorities may differ from others, but the truth is, each photographer finds their own way of sorting. The key point here is to just start organization early on.
There are relatively straight forward ways to store files by date, or by photo shoot name. I personally do it by subject. I'll have one for wildlife/flowers/people (within people I'll have a folder specifically for my kids)/events....etc.