So, in a couple of the example adventures there are NPCs who try to trick the PCs. My players are generally asking "is there anything dodgy about them?" because they're used to the Sense Motive system in D&D where a skill check is made after the event.

But I'm not quite sure how to do this. Based on the rulebook the idea appears to be to have them make an opposed Deception check, but if I roll that in front of the players they'll instantly know something's up.

Furthermore, according to the rules getting threat/despair on Deception checks results in "giving away a portion of the lie", so it seems I have to adapt what the NPC says based on the result of the roll - and then it's not clear if I have to make it totally obvious and make the NPC look like an idiot or try to put a subtle clue in and risk the players missing it.

How do people deal with this?

one of the best ways is to couch it in another kind of roll. IE they are searching a room and get some advantage and notice someone acting cagey outside...

I've wondered about this as well, and as far as I've been able to find out people have mostly been relying on either Perception or Discipline.

As an aside, an easy way to solve the classic problem of "roll against their Lie skill to tell if they're lying!" is to roll the difficulty dice in secret while the player rolls whatever skill you use for empathy.

For such checks, in any system, I tend to make these rolls in secret and before they actually interact with the NPC. Then I describe the scene as it unfolds based on the dice roll. But this method tends to require the trust of the players that you aren't going to screw them. Really, in many ways, social rolls of this nature really require the players to trust the GM and to go along with the scene as their character would even if the player might suspect something is up.

It depends on your group. If the players can keep player knowledge separate from character knowledge, it shouldn't really matter if you ask them what their vigilance is and then roll a dice pool in front of them, and then have the NPC lie to them (successfully or not). Some talents are specifically built around dealing with this, such as Unrelenting Skeptic.

If the players can't/won't separate player knowledge from character knowledge, then the GM may have to resort to rolling behind a screen/in secret.

Both of these have their pros and cons. I personally much prefer the first method, where players can run their characters with character knowledge only, but I understand that this is not always the easiest thing to do.

If they are asking whether he's being deceptive, roll an opposed check; don't explain the difficulty being put up. Just give them the dice, roll and narrate.

Sensing motives isn't a instant "I know everything you are planning" action, but rather success would give insight, fail would be a misinterpretation/non-read, advantage might be to gain some boost/upgrade on future social check as you notice something about their appearance/posture, threat is them noticing that you are observing closely and becoming more defensive; even men with nothing to hide become defensive after being offended.

The alternative is that you just don't roll until your characters have spoke to them. It's only after hearing the whole story that one party can think over it and identify whether he's being entirely truthful. Indeed characters making an insight check at best could only identify steriotypes and only one check should be rolled at a particular point, unless another member of the party has something to actually contribute toward the ongoing discussion.

Another thing about deception is that they don't have to be necessarily bare faced lying; a deception check can be about a fact that they have held back that they either deem to be of little importance or benefit on facial value, until paired with party experience.