Personally, I never use Sub Trim - never saw the need.

As far as Page 5 of the manual, it's a little vague.

What they are telling you is this:

First, set all of your trims to the center.

Then, place the servo arm on the servo so that it is 90° to the servo***


*** what a lot of people don't realize is that with Futaba servos, the servo arms are designed so that whenever you rotate to a different arm you will get a different angle (See illustration)