Hey Mark,
Either you create a G-code toolpath that uses multiple passes subsequently, or, if you strictly want a one-pass toolpath, I would use the 3-Axis Touch probe on top of the workpiece and probe Z, instead of lowering Z manually with -Z on Jog Pane.
No, it just moves Z. If you want to make the new position the new workpiece zero, you’ll have to click on the zeroing button for that axis, or enter
G92 Z0
into the MDI.