Ok sounds like your Z is correct, going up is a positive move and PgUp is normal for that, opposite for PgDn and the DRO moves negative. Same for the pop out, it is going the right way for Z by the sounds of it.
Ok for Homing the Z you move positive, this will, when it hits the switch and backs off set the Z machine coords to Zero (make sure you dont have a value in Home Off box) Then for Z Soft Limits you set 0 as Z Max. Z Min is set to the axis travel but as a negative number, so if you have a 6inch travel then Z Min will be -6.
Hood