Lots of questions there, I will try answer a few while I have my coffee
What should happen during homing is that the axis will travel towards the homing/limit switch (in your case if you want to use the same switch) then once it activates the switch it will move off, then travel once more towards the switch slower, activate it once more then move off and stop.
The idea is that the machine then knows how far you can travel without hitting the end (mechanically)
Hitting the switch by hand is probably not the best idea as emc thinks the homing/limit has tripped while moving away and thinks something is wrong, maybe you have to set the travel from home switch distance to something smaller so it comes back sooner for the second time. My machine has a buggy limit/home switch so this happens sometimes for me as well, I just have to click it a few times to sort it out.
You can set all the speeds for this in stepconf.
Unfortunately if you don't get the homing right then running jobs will be hit and miss to say the least. You could possibly home manually for a start, I have a couple of small machines I do this with as I am too lazy to wire in the limits. Simply move each axis one at a time to its minimum travel and press the home axis button. To do this you will have to not set the switch to homing during stepconf setup, otherwise you will not have this button.
The Z axis is a little more tricky as you want Z0 to be at the top of its travel and travel in a negative (or down) direction from there, so the directions can seem back the front.
Oh yeah while you are playing around with all this make sure your estop is working properly, you will most likely need it in a hurry at some point !
I am away from my machine so I can't give you the specific settings for my machine to help just yet, but I can once I get back.
Hope this is some help, I will follow up with some of the rest later, I have to head out the door right now.