First things first: do you give your PCs automatic sense motive rolls when an enemy is trying to bluff them? Since bluff is an opposed roll vs. sense motive, if you don't give them that, the only way to avoid having all NPC bluffs automatically succeed against characters and players is to constantly ask the DM for sense motive checks.
This is often contrasted with "role-playing it" but that has always struck me as an incredibly dubious proposition. First, DMs often role-play people who are better or worse liars than they are. Second, players often role-play people who are better or worse judges of character and people than they are. So, there's an element of both "wow, our DM is really smoothe, we'll never be able to figure out when his NPCs are lying and when they are telling the truth" and "well, that's a pretty obvious lie, but my 7 wisdom rogue is a sucker for beautiful women and a horrible judge of character, so I'm not sure he'd notice the inconsistency; what should I do?" And, more to the point, nobody is so good an actor that they can accurately and reliably portray the differences between a scared low-life who's a lousy liar, a scared low-life who's been fooling people his entire life but right now is so scared that he's out of his depth, a low-life who isn't really scared but wants the PCs to believe that he's scared and a bit out of his depth so that they'll catch his "lie" and believe him when he tells them the "truth" and the the NPC who isn't even a low-life but wants the PCs to believe that he is an example of the first kind of NPC, and not only do that convincingly, but do it so that a person with a wisdom bonus can figure out the first case but will be fooled by the rest and the player with a really high sense motive will be able to catch all of them except the last. It's not going to happen. If you're going to have mechanics for social skills at all rather than simply pitting the DM's social skills against the players' you need to use them.
So, what I suggest is collecting the PCs' sense motive skills and rolling them behind the screen or behind your hand every time your NPCs are bluffing them. If the PCs succeed, pass them a note with something like "you don't think he's telling you the whole truth" or "he seems to be hiding something." If the PCs fail, don't tell them anything.
The other uses of sense motive are much easier to adjudicate. You might want to roll the sense enchantment uses for the players, but let them ask if they can get a hunch about NPCs. Hunches are things like "this guy seems to be on the level" or "Pholtarin is completely unhinged; there's no telling what he'd do to achieve his goals" "for all the warmth and folksiness he's trying to project here, you don't think this guy is really comfortable outside of elite, upper east side circles."
