Ok, I labeled the gears in the pic below. It looks rare that you'd need to change the spindle gear, unless you cut alot of coarse threads. Using the 1st Stud as an example, the large gear is the Driven gear and the small is the Driver. It's the driver because it's what's driving the next gear in the train. On the 2nd stud, you can't see the Driver gear because it's behind the Driven.
So to cut say a 32 TPI thread, you'd leave the spindle gear at the 20T gear that's there now. On the 1st Stud you would pair a 40T and a 25T gear together and set them so that the 40T gear meshes with the Spindle gear. Put a 50T gear on the Lead Screw to mesh with the 25T gear on the 1st Stud. Adjust the banjo (the thing that the studs mount to) and the stud to make everything mesh.
If you were doing a 16 TPI thread, note that there are no gears on the chart for the studs. Fit one gear on the stud to mesh with both the spindle and lead screw gears. That extra gear is referred to as the Idler gear.
On occasion, you may find the Lead Screw gear is in the wrong place to mesh with the Idler, there should be a spacer on the lead screw that you'd move to either the front or back of the lead screw gear so they will align. One time that would happen is when you switch from 16 to 32 TPI setups.
On those occasions where you only need one stud, just remove the 2nd stud and set it aside. If the 1st stud won't move far enough to mesh with both gears, move it where the 2nd Stud would go.
Hope that made sense.