I just ran my first session and it went fairly well but there was some confusion about combat. When PCs roll they can use advantage if there is a net advantage and if there is a net threat then the GM can use that but what about for NPCs. If there is net advantage on an NPC roll does the GM use it ? If there is net threat from an NPC attack do the PCs use it?

I'm not sure that players spending threat for opponents is actually stated anywhere in the rules, but I think that is the intent (as always, with the GM able to overrule the PCs if they choose something that doesn't fit the story) and that's the way I'd rule it.

Page 132, Resolve Advantage and Triumph, and page 133, Resolve Threat and Despair says the active player chooses how his character spends advantage/triumph and the GM decides how to spend threat/despair. However, it does go on to say that the GM can let the players spend the threat generated on NPCs rolls.

-EF

This system encourages player participation so much that it's awesome. I'd say go with the rules stated above and let the player spend the Threat rolled by NPCs against him or her. It's like Attacks of Opportunity except more fun.