If this is for RMFRP/RMSS, you actually have no penalties for using the trained weapons in the trained hands. Your number of ranks in TWC may not exceed the number of ranks in the weapon skill for either weapon. Your OB is based on your skill bonus in TWC and not on your skill bonus in the respective weapon skills. You suffer a -20 penalty if using the weapons in the wrong hands (e.g. your skill is for rapier in your right hand and dagger in your left hand, if you have the rapier in your left hand and dagger in your right, you suffer -20 for both attacks). You also suffer a -20 penalty on both attacks if attacking two different opponents.
If parrying, you reduce both attacks by the same amount, and that amount is your parry DB. E.g. if you have +85 OB, you could make two attacks at +65 and gain a +20 parry DB. If you attack two foes, you are starting with +65 OB (+85 minus 20 for two foes), but you could make two attacks at +45 and get +20 parry DB against each foe.
The idea of skill bonuses canceling out penalties is an RMU thing, it doesn't appear in RMSS/RMFRP. I'm not sure how this works in RM2/RMC, that might be different from both.