Ok, this is kinda complicated so get ready for a wall of text:
Autoattacks alternate between the left-hand weapon and right-hand weapon. Most abilities in the DW tree will generate 2 hits (for example flank attack hits once as your guy dashes past the target and again when he dashes back behind it); one of those hits is dealt with the left-hand weapon and the other with the right-hand weapon.
For each hit, the base damage is based on the weapon used for that hit. So for example if you have a dagger in one hand that deals 50 damage and a dagger in the other that deals 100 damage, your autoattacks will alternate between 50 and 100 damage (ignoring for the moment your other stats and enemy defenses, armor, etc.). Likewise, if you use Flank Attack, you will hit once for 50 damage and a second time for 100 damage.
Similarly, if you have a dual-blade dagger in one hand and a regular dagger in the other, only attacks made using the dual-blade dagger will deal AoE damage. The same goes for runes: if you have a rune on one of your daggers, the extra damage that it adds will only be applied when that dagger is used to hit the enemy.
However, all stat bonuses (attack%, crit%, +crit damage, +dex, etc.) on a dagger are applied to the wielding character as a whole. So if you have two daggers equipped, each with +5 crit%, your guy gets +10 crit% with each and every attack.
Likewise, any masterwork bonuses the daggers have apply to your character as a whole as well. This includes the bonuses that proc on hit. So if you have one dagger that procs Hidden Blades on hit but the other dagger does not, you still have a chance to proc Hidden Blades on ALL attacks, no matter which dagger was used to make the attack. Yes, this means that DW rogues can have up to 3 separate active masterwork bonuses (one on armor, one on each dagger) at a time and fully benefit from all of them. However keep in mind that masterworks don't stack when planning your crafting.