Save fixture is saving the G54 or whatever Coordinate your workpiece was before you shut down Mach3.
If you do not save it, you will have to re-zero you work or vice before continue your job.
So if you shut down Mach3 and you are not finish with your work, say yes to Save Fixture.
For the new computer, you can save or copy your XML file and place it in the Mach3 folder in the new computer.
What I do, when every thing is setup correctly, I open each of the port and pin windows and press Alt + Prt Scr (print screen) and paste the image in a word processor
(like word pad) and print it. Next time, will be easy to setup every thing like it was before.
Here's an example of the the copy I have for mach3 setup (not the real one)
Jeff