Hal files: MesaCT vs. PNCconf - help please

I have a VERY fuzzy picture of how .hal files interact with LinuxCNC.

I'm using Axis with a Mesa 7195t

My limited (possible incorrect) understanding is as follows:
1) hal files act as a txt file based definition of how various hardware points (inputs, outputs etc.) are configured and linked to the LinuxCNC software
2) hal files are/can be generated by using configuration programs  such as PNCconf or MesaCT, or they could be written from scratch or edited with a text editor.
3) If a hal file generated by PNCconf or MesaCT is edited with a text editor to add functionality that functionality (lines added using the text editor will likely be lost if MesaCT or PNCconf is used again to tweak or add some other functionality.
4) I think when LinuxCNC starts it reads the .hal files to know how to interact with the hardware?
5) I think there can be multiple .hal files that get read on startup?
6) It's really unclear what type of configuration items go in what.hal files or how one would know which .hal file and where in that .hal file changes should be made?
7) I presently have a io.hal as well as a main.hal that were generated by mesaCT. I'm not sure if I should also have a .hal file generated by PNCconf?
8) I would like to assign encoder0 to a linear scale (hopefully that I can then view somewhere in Axis to see if I have the scaling correct and compare to my external DRO.

If any of my assumptions above are incorrect, please let me know.

Much appreciated