When I made my first attempt to write a novel keeping track of the manuscript was easy. I had a single file on computer where I did all my writing. As long as I saved my work at the end of each session I had no problems.
At first I did all my writing at home. I had a computer at work but lacked the time to write there. Eventually I wanted to be able to write during the down times but couldn't because my PC didn't have Microsoft Word and I didn't want to pay for a copy. I started using one of my blogs as a writing platform. All went well until I tried copying and pasting from the blog onto my home PC. In a few words: major formatting issues. Not that I couldn't overcome them, but it took time. Lots of it.
I started bringing my laptop to work. I had plenty of desk space and, as it happened, more time to write. That was fallout from the economic recession.
Change happened at work and our computers got upgraded. Now I had Word on my work PC and I could write fiction when time permitted. New problem: how to collect everything into a unified file. By now I had joined a critique group and it seemed I was always making new files of chapters to send to the group. Unwittingly I found I had created a monster. I had multiple files of the same material--well nearly the same. If I made changes in a chapter and didn't update the files the same way I had no way of telling what was the best.
Solution: more time spent perusing the myriad files and culling the bad from the good. Now I have one master file containing my WIP as presently revised. Everytime I add to it I make a copy, email myself so I can update the workplace copy and vice versa. So far it seems to be working. For the next book, things are going to be different from the get go.