It would be a waste of having a good hit chance if you put BAM on your Primary weapon because then you will have a setback die.
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There aren't any setback die.
That is wrong, by my reading of the book. It assumes you aren't trying to hit with your secondary weapon unless you generated enough advantage to, but as soon as you declare Two Weapon Fighting rules and add the extra difficulty, you should be taking into account the second weapon as your character is firing it. To my knowledge, the only exception to this is the Bantha's Eye, as it specifies a successful hit, so you don't gain it's advantage unless you trigger the offhand hit. Superior, the drawback to the Blaster Actuating Module, and Accurate/Inaccurate all take effect any time the weapon is fired.