Always as primary. Despite the fact that you are wielding another off-hand weapon, you are treated as one-handed, shield-less combat, as long as you declare it.
The loss in attack bonus is not given because of your 'bad' arm, but rather because you are constantly focusing both weapons, both arms, and the motion is very harder. This is why your readings of enemies are slower, and so you miss more. You are also more worried about disarming and etc etc.
Just remember to state beforehand in your turn that your next attack will be considered a one handed attack. If you do so, understand that until your next turn you are one handed. This also means you lose any other bonus inherited by dual wielding skills, such AC or reflex from some feats.
Also: As long as all your off hands match weigh limitations, any hand can become your primary. Easy with dagger/dagger because your offhand is always a light weapon. Since a mace is not a light weapon, it MUST be your primary weapon whenever dual wielding, unless you have proper feats to wield non-light weapons in your offhand without huge penalties.