Hey Jordan,
me personally would always have the probing in the g-code file, and make sure that the ‘tool-change’ routine suits my needs, as explained here.
But generally if you don’t have probing in the g-code file, I would do probing before running the g-code file. As always, you must ensure that your real zero position that you are probing matches the workpiece zero position (aka part origin) in your 3D model.
Onefinity has made these videos for probing:
I assume that since you want to mill lower than your wasteboard surface, in your 3D model, you forcibly must have set the workpiece zero (aka part origin) on top of the workpiece? Assuming that the wasteboard is modeled as the workpiece.