The easiest "manual" method I found is to just hand-tighten the collet nut such as the bit won't fall out, but can still slide a little. Then drop your Z down until the bit touches the material, and go a little more so the bit actually slides into the collet a small amount. Zero the Z, then you can finish tightening the collet nut with your wrench. Depending on teh job, you might find that getting close, then PULLING the bit down to the work, might be easier, for example, with a long bit.
Another way: Shut off your drive box, and manually drop the Z down. You'll feel and hear the bit touch the material. Turn on the drive and Zero the Z. Will get you to within one step, which is pretty close depending on your screw pitch.
There are times when I have to machine a board with an uneven surface, but want an accurate thickness relative to the back of the board; for example rabbeting the edges for a groove. Or I have boards of different thicknesses that I need to be the same thickness at the edge to insert into a tenon. Once I surface the spoilboard, I'll zero the Z out to the spoilboard, then go into the MDI and move the Z up to the nominal thickness of the boards, then zero it out again.
You can do the opposite, if you have a workpiece where you cannot mar the surface. I get a scrap piece of ground aluminum plate of known thickness, and zero out to that. Then I go into the MDI (after moving the cutter away from the piece) and bring it down the thickness of the plate and re-zero.