I know its probably a little late but I came across this same issue last week. If your using a FIZ 2 hand unit then you will have to create duplicate marking disks for each lens. One for when your wide open (Blue mark), and one for deeper stops (Yellow mark). If your using a FIZ 3 however its much easier. With the FIZ 3, after the motor has calibrated you then tell it where infinity is, and then it lines up all the marks from that (given you have correctly added/calibrated each lens at the prep). Depending on the stop, simply line the Infinity mark either to the yellow or blue mark, depending on your stop, and then all the other focus marks will line up to that same mark.
I also discovered that the focus mark will shift between the blue and yellow mark depending on your stop. For example say if your stop is 2/2.8 split, your focus mark will be in between the yellow and blue marks. With a FIZ 3 this is easy to adjust, simply set your infinity mark in between those two marks. As Chaz mentioned on a FIZ 2 you can move the mitnes mark on your preston (with some tape) to line up with the appropriate mark.