The menu shown in your screenshot controls the general direction of movement. Set it so that the machine moves correctly when you press up/down/left/right/PgUp/PgDown keys.
Homing is set up in Config - Homing/Limits menu. There is a tick mark labeled "Home Negative".
P. S. Also, your pin numbers don't seem to be set correctly.
You said you have 1 switch on the X axis - then why do you have both X++ and X-- set in the menu? Same goes for the Z axis.
On the Y axis, do you have one switch on each side of the portal? Why are they both wired to the same pin? That could make automatic squaring of the portal a bit problematic. Also, same problem with Y++ and Y--. You really have home switches, not limit switches, so it would be best not to use X++, X--, Y++, Y--, Z++ and Z-- at all.