I have also been having some trouble with making an item. I’m trying to make a wondrous item for a monk that give him +1 bonus to hit and damage with unarmed strikes and deals an additional 1d6 damage but the only thing I can get to work is the bonus and not the extra damage die 

That is not something that the system can currently do. It cannot combine those dice from the multiple sources and roll them together automatically. The player will still have to roll the additional die separately and manually.