Print calibration script (File→Scripts→Calibration→Replicator 1&2→Dual Nozzle Calibration.gcode).
When it does start, you’ll see it print a series of straight lines parallel to the front of the build platform, starting at the front left corner of the platform and extending back. The second series of lines will be perpendicular to these, and will start at the center of the platform and extend left.Then the second nozzle will print a set of lines alongside each of the first two sets. All four sets will have 13 lines, with the first line being longer than the others.
If you look closely at the paired sets of lines, you’ll see that the first lines in the second set are a tiny bit in front of those in the first set, while the last lines are a tiny bit behind. Somewhere you’ll find a line from the first set and a line from the second set that match up almost perfectly; that’s what you’re looking for.
The longer first line is line 1. The middle one is line 7, which is the default. So if, say, you’re looking at the set of lines on the left side of the platform and you decide that the line just before the middle one is the best. Input the best line number into “Setting→14. Calibrate X / 15. Calibrate Y” in machine control panel.