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.

Your decision can be a lot easier if you have some stats on your opponent. If you know he bluffs a lot then it's a pretty easy call and obviously +EV. If he never bluffs then it's a pretty easy fold on the four spades board. If it's on 3 spades board then you unfortunately have to call if he bets into you.

it depends on the position
if your oppenent bets you call and see the turn, if you are in position you either check or cbet, since you have to mix those stratiges anyway
you can't fold your sets on board just because it had 3suited cards, and you are almost never dead in such scenarios, so play as usually

it all epens on other stack size if am firs to act i will just bet te blind if i am last to act some one gots pot i will fold

On monotone boards, I think you should generally go for a small cbet around 1/4 pot. This charges their draws and gives your opponent a chance to raise you. If the turn and river is clean, you should bet larger as many of the stronger hands would have raised flop.

If I'm not mistaken on monotone boards we are supposed to bet with a larger bet.

I just had that situation and I bet 2/3 of the pot on the flop with my set of jacks