Damn. Unfortunately, I don't know the mechanics well enough to really help with encounters from a design standpoint.
Where do you want the plot to go? What do you want them fighting? Those are probably the biggest things to worry about when designing encounters.
Other things you can consider are, essentially, cheating. But as a GM, sometimes you need to do just that. In your role as GM, roll where the players can't see it, and don't be afraid to fluff the rolls if needed. Yes, this may require Bluff checks, and I know Charisma isn't your strongest stat (well, I guess it's Manipulation here, but whatever). And don't be afraid to Deus ex Machina if absolutely necessary; I've had to do so before, and I'll probably need to again eventually. However, a Deus ex Machina needs to be planned ahead of time. Don't suddenly introduce a faction to save the day unless that's needed specifically to introduce that faction into the story. Engineer events to suddenly make it harder for the enemy or easier for the party (cultists hurling smoke grenades has worked for me, though that's a different system.) Improvise.