Trainer mode on stock software confusing and I actually couldn't get it to work. Er9x trainer mode makes it really easy.
With er9x you map incoming channels to the function (RUD, THR, AIL, ELE), for each incoming signal you can switch Off (ignore), Add or Replace Trainer throws, Percentage throw control, and finally assign to which switch, normally the trainer switch but you could select one of the on off switches if you really wanted to.