Problems continue and don't know what to do

[JAZZCNC]

I also have X going in reverse.

If you have the Motor phases wired correctly IE A+ A- B+ B- and the drives wired Correctly IE: Step+ Step - Dir + Dir - then don't switch the active Hi / Lo because it can cause other issues with pulse edge etc depending on how drive is setup.
The easier way is to go into Homing / Limits and toggle Reversed, this will reverse the axis but not affect Pulse and Dir. You may need to toggle the Homing direction as well if it goes wrong way when homing.

So I have a question: When setting up the steps, when I tell it to move a distance and then it asks me how much it actually moved, should I have told it that moved in minus? I simply said how much it moved and didn't think anything of it at the time.

No doesn't matter. only needs to know distance moved.

I've written my settings down too, on paper, so should something ever happen, or I adjust something and need to un-adjust it, I have something to reference.

Thats always a good idea but when finished setting up also make a copy of the XML file which will be in Mach3 folder under same name as the profile name. Then if goes down at any time you just reinstall Mach3 copy the saved XML into folder and it will reload with all your settings ready to go.