Yep, there are no rules against using unarmed strikes with Two Weapon Fighting and Flurry of Blows at the same time in PnP.
Quarterstaves are considered a double weapon in PnP, which allows you to use the TWF feats with it for more iterative attacks. The same penalties apply as if you were attacking with a weapon in each hand, and you do 1/2 str damage with the "off hand" attacks.
The problem is DDO isn't coded yet to take into consideration double weapons.