Upvote:1
Japanese visa applications are processed by actual humans, so you can eg. write both dates of arrival in the form, state purpose as "Transit x 2", and note that you want a double-entry visa in the "Remarks" section of the application.
In my experience, Japanese embassies are both very meticulous at following rules and helpful at advising applicants how to apply "correctly". Since every embassy/consulate has its own slightly different procedures, it's usually a good idea to call the embassy or even better go there in person and ask how to apply -- they'll help you out.