I tend to treat knowledge skills a bit differently from other skills in that often the "penalty for failure" in a knowledge skill is that the game stalls because of that lack of knowledge. So I tend to use a GUMSHOE-inspired mechanic where just asking for the knowledge check with a particular skill is sufficient for a PC to get a baseline level of knowledge (enough to keep the game going) and then the better they roll the more depth or breadth of an answer they get. So if they have two skills that are relevant then I'll tell them to pick the one with the higher bonus but then bump them up to the next level of knowledge based on what they get on the roll (though a roll of 1 means that they only get the absolute minimum[*] and don't get a bump up at all). So for example if the players find a ruined shrine and failing to have that answer would stall the game (for whatever reason), then just asking me for a Religion or a History check is sufficient - even on a failed roll - for them to determine the name of the ancient obscure power whose shrine this was. But if they have both skills then I'd give them the information I would have handed out for the next better roll (like maybe on a minimal success I'd normally tell them additionally that this obscure power had a bloodthirsty reputation). And better rolls would get a bump up on the info (though at some point they just get "all of the information" and the extra skill doesn't really help them much).
For the more action skills like Athletics or Acrobatics I get annoyed at the overlap and irritated at being reminded of it. Then I give the player who took both skills advantage on the roll because it's usually the rogue and so there's not much harm in it.
[*] Or more typically when I can pull it off - a wrong answer that will keep the game going but play out for comedic effect at the right moment. My long-standing group of players are good with running with the "our wizard-historian says that King Feledes was a kindly king so that's how we're going to play it" even when he's rolled a 1 and they know it's probably wrong because they know that it'll be funnier when I eventually pull that 1 back out and the historian is proven wrong. Though they can't always count on it since sometimes I do give somewhat truthful, if minimal and sometimes twisted, information even on a roll of 1. Just to keep them guessing - I don't think they should just assume that a failed roll means that the opposite of whatever they think is true is the actual truth. It should be wrong, but contain enough truthful info that they know enough to not trust anything about it. Tough to pull off sometimes, but when it works it works.
For the more action skills like Athletics or Acrobatics I get annoyed at the overlap and irritated at being reminded of it. Then I give the player who took both skills advantage on the roll because it's usually the rogue and so there's not much harm in it.
[*] Or more typically when I can pull it off - a wrong answer that will keep the game going but play out for comedic effect at the right moment. My long-standing group of players are good with running with the "our wizard-historian says that King Feledes was a kindly king so that's how we're going to play it" even when he's rolled a 1 and they know it's probably wrong because they know that it'll be funnier when I eventually pull that 1 back out and the historian is proven wrong. Though they can't always count on it since sometimes I do give somewhat truthful, if minimal and sometimes twisted, information even on a roll of 1. Just to keep them guessing - I don't think they should just assume that a failed roll means that the opposite of whatever they think is true is the actual truth. It should be wrong, but contain enough truthful info that they know enough to not trust anything about it. Tough to pull off sometimes, but when it works it works.