If you want to master jobs on story characters, do dispatch missions with non-story characters, this gets you AP for everyone and EXP for your non-story characters.
If you want to master jobs on non-story characters, do normal missions and use your story-characters (or a mix). Your story characters get exp, and everyone gets AP.
I don't religiously do this, but I try to level up on the best jobs whenever I can without it taking too much effort on my part. <.<
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