Have them roll a skill check in every hex -- probably one check, though other players can aid another if they want. If they're not looking hard, they won't find whatever it is.
If you really want them to find a location, you can always drop hints (bandits with treasure maps, random questgivers, tracks).
If they don't find the hidden location and clear the hex, then maybe there will be problems later when they come to settle it (a forgotten wight bursts out of the barrow and slaughters a village, bandits operate out of the ruined temple, etc., etc.)
I'm getting ready to run Kingmaker as a GM, and I was wondering about something. Hidden locations require a certain skill check to discover. How did you do that?
Let the players roll one skill check when exploration of a hex is complete? Let them roll one skill check each? Roll skill checks more than once during the exploration? Roll hidden skill checks for the players?If I let the players roll the skill check they'll know that there is something there to be found even if they fail (unless I require a skill check on every hex), but if I roll the checks secretly, I feel I'm taking a bit of agency away from the players.
Just let them roll on hexes where there's something to be found.
I ran Kingmaker for a group of mostly novice players, and at first it annoyed them that they knew something was there and they wanted to "search again", but I just explained to them "Part of role-playing is separating player knowledge from character knowledge. Your characters think they have fully explored the area, so they're not going to spend days searching it again and again, just in case".
Some of them took a little bit longer than others to wrap their head around that and get over it, but unless you want to end up rolling a d20 to search for secret doors every 5 feet of corridor just to fake out the players, or for you to roll all the PCs skill checks in secret so they don't know how well or how poorly they've done, it's something they'll have to come to grips with eventually.
As for method, I let everyone capable of making the skill roll (ie only PCs with ranks if it was a trained only skill) make the roll and took the highest result. If they want to have one person roll and use aid another, that'd be fine too. I'd just try and be consistent.
Personally, I assume a 'take ten' search roll for my players when they enter a hex to decide whether they will find something on a general search. If they do find it, I can RP the approach with them.
Even if they fail, I throw out a few clues for them to follow up, if they want to, or they can ignore if it doesn't interest them. It might generate a more traditional roll later, or might just mean that I give them bonuses to another Take Ten :)
I also throw out a number of 'false' clues as well, so they don't obsessively follow every hint that I give them :)
In my game, there are a number of NPCs that are used to support the party and I let them find the locations (and keep any treasure) later in the game - once the party have stopped showing an interest in an area.
Also, there's more than one reason to make a Perception check. The players are exploring a hex, the GM calls for a Perception check and everyone rolls poorly. Does that mean there's something in the hex they missed, or does that mean that they're about to be ambushed by a wandering monster? In fact, intelligent or cunning enemies might stealthily tail the party for a few days before attacking to learn about their strengths and weaknesses, to wait for reinforcements or to wait until the party is damaged from another fight... maybe they were rolling Perception to notice the tail, and so even when an ambush doesn't immediately materialise, it doesn't mean they were obviously rolling to notice a hidden feature of the hex.
Something I planned in my game was to re-purpose rolls on occasion. I wrote down the difference between the Survival and Perception skills of my players, and the idea was that when they were foraging for food or whatever and made daily Survival checks to see how much they found, I could adjust the number to treat the roll as a Perception check instead. I didn't ever actually use this idea though, because my players seemed happier to simply load up their horses with mountains of rations and never go slowly to forage.
Maybe the perception check was to notice a black dragon flying over the Narlmarches near the horizon, or to spot some tracks that if followed could have led to a small band of bandits/kobolds/mites ranging far from their normal locations. There's any number of reasons that a failed check doesn't mean that you missed something in that specific hex, and the sheer size of each hex (~100 square miles!) means that there's always plenty of room for additional things to find aside from what's officially there. Pick a couple of relatively high DCs and let the party find stuff even if there's 'nothing there'. Reward them for being highly perceptive by noticing a camouflaged hunter camped out in a blind, or an overgrown ruin of a house from when the region was settled, or just an encounter with a benign type of fey or other such creature (perhaps a pooka or mockingfey?)