How to play a flopped set on a 3-suited flop

I ran into this situation earlier and got in a lot of trouble, but I feel like this is one of those (fairly) straight forward spots where there should be a clear answer as to what's the best EV play as far as betsizing etc. is concerned.

Assuming hero is in position with a small pocket pair like 6c6h, the flop comes 6s9sQs. Obviously this is a huge reverse implied odds hand so how do we extract the most value from this position and what's our plan?

Do we just size our bet assuming villian has only one (high) spade and make sure to reduce his implied odds enough that he's reluctant to call? The problem with that of course is that if he already has a made flush we are just spewing chips, but maybe this is one of those spots where that's just a risk we have to take? The chance of villian having two spades is only around 3% chance after all. If another spade comes after villian calls I assume we just have to give up or go into bluff catching mode but if it doesn't come then what do we do on the river after betting both streets. If villian comes out firing on the river do we have to call his bet assuming it's a bluff?

We just make a standard C-bet, and its totally fine, if he call with a 1-card flushdraw, because we are pretty far ahead of that kind of hand. Also if another flush card comes without the board pairing, our situation is pretty easy. Our hand is clearly degraded to just a bluff catcher, and against a lot of players bluff catchers can just be folded to serious aggression. So the only difficult thing here is to get past that feeling, that you "must" win the hand, just because you flopped a set.