Jim' the WinCNC guy, but I'll take a stab at your Q's.
1)
a) don't program parts bigger than your machine.
b) Hopefully the machine has limit switches to stop it from running to far.
c) If no limit, ahopefully at least soft limits.
2) Soft Limits are basically limit switches in the software to stop the machine from going to far. Not sure if WinCNC supports them. One thing about soft limits. If you don't have home switches and use them to "home" the machine, soft limits won't work, as the controller (WinCNC) needs to know where its at so it can know where it needs to stop.
3) Not sure, but usually you touch the tool to the top of the workpiece and it sets that as Z=0. It doesn't really know where the table top and /or spoilboard are. It's up to you to make sure you're programs don't drive the tool into the table, unless you have limits to stop it. Usually soft limits won't help you here.
4) When you create the toolpath, there's a "Tool" section in the toolpath dialog. Select "edit" in the tool section and those settings are in the window that opens.