Differences Between Mach3 Mill and Mach3 Plasma?

I have been using Mach3 for several years now on my CNC Mill and on the CNC Gantry Style machine I've built myself. My first self-built gantry was made of MDF and had only a wood router. My new version is metal, much faster, and it will have a plasma cutter attachment in addition to a wood router.

My question is related to the difference between using Mach3 Mill and Mach3 Plasma. I have been searching the net, as well as CNCZone for info related to using a plasma cutter with Mach3 as opposed to in a milling configuration, but haven't found the answers I need.

I'm still confused mainly in regards as to how Z height is handled. I know that I must use some type of Torch Height Controller that should adjust torch height to maintain a proper voltage for the arc, but how does that interact with the Z coordinates specified in the GCode? In other words, when I am writing GCode, do I tell the Z to come to a specific distance from the work and then let Mach3 make "fine tuning adjustments"?

Other than the above questions, if anyone has links to other posts or other internet sources specific to using plasma and mach3 I would appreciate it!