Um. Seems complicated. Perhaps I didn't get it ? Here's what I do.
1: Print the first target. Quit ColorMunki Photo.
2: Allow the target to dry for 24 hours.
3: Re-open ColorMunki Photo. When you come to print the first target select the 'I have already printed the test chart' option. Scan the target.
4: Print the second target. Quit ColorMunki Photo. Allow the second target to dry for 24 hours.
5: Re-open Color-Munki Photo. When you come to print the first target select the 'I have already printed the test chart' option. Scan the target.
6: 'Print' the second target but cancel the print dialogue or delete it from the print queue (as described above).
7: Scan the second target.
8: Bob's Your uncle (or somesuch).
Methinks a nice idea for X-Rite to consider would be a "I have already printed my TARGETS" option so, having printed both targets (as above) you could just scan them in without all the printer gymnastics. "Simples ?!".