Printing handwritten notes is controlled by the Note Printer setting in the your note's template settings.
If Print with Labels is selected, then the note will be printed along with the main shipping labels.
If a specific printer is selected then the note will always be output to that printer.
Notes can be generated in 2 ways. Using the rules or by using the right click menu in the advanced dashboard. When using the rules, the note will be generated and printed at the same time as your shipping labels.
Alternatively you can generate notes by right clicking on a shipment in the advanced dashboard then clicking Generate Handwritten Notes and then clicking on a template.