So, now you know what bits are what in the interface, what about the files?

More interestingly; what hapens if you break something... Which is easier than you might think.

What are the files?
There may be a couple of other files kicking about too if you do some weird stuff. Like a .TODO if you are organised (I think that one is self explanatory...)

And what do I use?
Well, the .pas files are what get loaded into the editor. So, you use these all the time.
If you accidentally delete a large wad of code, then you have several options...
There is an issue with some component that seems to exist.. or doesnt.
This happens after reverting to old .pas files or sometimes if you randomly delete stuff that you probably shouldn't (It happens, by mistake, often).
Hopefully this won't happen. It can do if your it crashes part way through a save, or if you mess about with the lists.

Another problem is versioning...
If you are sensible, you will make backups. This is good. However it can cause problems;
You should not have any other real problems with the files and saving and such. If you make a backup, zip it or something because pas files floating around all over the place is horrid. I always save like this:
ProjectsFolder                      where all the projects are
    NewProjectName             the new project you are working on (save the PROJECT here, not the units)
          Units                           put units in here! Easy.
That will save a lot of bother, trust me.

stringfellow wrote this guide