Probing help

[timmcg3]

I've recently built a PrintNC router and I am using axbb-e and uccnc. I'm having a lot of difficulty getting probing to work. For my probe I have + connected to the spindle and + to the input connected to the workpiece.
I'm trying to make some simple aluminium parts out of 12mm plate. This is what I have been doing:
Import program from f360. Jog over to my workpiece and lower tool until its reasonably close. Hit the 'Probe' button on the main screen. When I do this the z axis moves up until the machine coordinates z are at -100, I'm not sure why.
To get around this I have just been manually touching off on the workpiece with a piece of paper, then zero all axes and run my program.
Program finishes, I then jog up, change tool (with a different length) and load a new program (2nd operation same part). I then click 'go to zero' on the x and y axis and then click 'probe' on the main screen. Z axis slowly moves down until the tool touches the workpiece, backs off, repeats that and the goes to safe z height, So probing appears to work. However when I start my program the spindle goes to the original z zero not the probed z zero, causing me to either machine air or snap endmills by sending them far too deep. How do I get the probed value to be my new z zero?
Also the probing tab has me very confused. I click on 'simple probe' then 'z axis' and then start probing. I get no movement anywhere and just says 'probing' No matter what button I push here I cant get anything to work.

For reference I have no experience with cnc. Building and wiring my machine was easy, but the software has me very very confused. I have watched several hours of videos and read all the help pages but I think that made me even more confused.
Any help would be much appreciated
Thanks, Tim