If you use the handheld torch, you will have to figure out how to bypass the safety circuit (it is not that difficult) that is designed to prevent the torch from firing from a remote start interface, as opposed to the trigger switch. Hypertherm employees cannot supply advice on how to bypass this important safety feature.....as it is a safety feature!
If you use the machine torch, and have a unit with the optional cnc interface plug on the rear panel, then interfacing the system is safe, simple, and quite easy to figure out. The machine torch is easier to square to the plate, and is generally easier to route the leads from. I use a machine torch on my Powermax 45 that is mounted on a PlasmaCam machine, when I wnat to hand cut I unplug the machine torch and plug in the hand torch (less than 10 seconds) and I'm ready to cut by hand.