Well, I finally made the machine carry out its first cut just now and nothing went horribly wrong thankfully.

First things first, I made mounts for 3 home switches and fitted them to the zero positions for the machine on all axes. Wired them up and set them up in Mach3. They're currently set as active high because I didn't have any NC switches to use. Will get some though as I think it's a safer option in case a switch fails.
So they're set up, I have referenced all home on the machine co-ordinates, and nervously watched as each axis homed itself to the switch and settled just off them. Phew.

I did briefly confuse home switches with limit switches at one point, where the soft limits where switched off, an axis hit the home switch, and carried on, without me immediately realising why. I realised quickly that it was because the soft limit button was disabled. Is there a way for the home switches to also be physical limit switches as well, or would that not be a good idea?

Anyway, I fitted a 5mm mill attached a vise with some wood in it, and jogged the table over to the wood and the head dropped down until it touched the material, then zeroed the work co-ordinates.
Next, I opened one of the wizards - shape wizard, then set it up to cut a circle. I'll be honest that I didn't expect nearly so many settings for this, and wasn't sure what several of them were for as such, so I set very low figures and hovered over the Estop!

So I told it a 10mm radius circle, and the resulting circle is 25mm wide. It's using a 5mm end mill, so it seems the centre point of the mill is where the cut circle is measured from. I guess I've missed some sort of offset, or set it wrong to account for the diameter of the mill so that it ends up actually being a 20mm circle instead of the 25mm it came out as.

Also, I set the plunge and depth as 3mm but am not sure what the distinction is here? I also set the horizontal offset each as 1mm. I wasn't sure their purpose but when it cut into the wood it cut one shallow circle, then dropped very slowly lower & cut a second, then repeated this pattern for a third. I'd have to guess the vertical offset is like a divisor in this case for how it layers the 3mm plunge or depth into 3x 1mm deep cuts?
Not sure what the horizontal offset did though....?

But anyway, it worked nicely, even if I was ready to hit the stop! Video'd the second run of it once I realised it wasn't going to do anything horrible.