I think it comes with practice.
I am where you're at basically, I just use as rule of thumb that a flush draw on next card is close to 20 % probable, gut-shot draw less than 10 %, open-ended twice that etc. What I have difficulty in calculating is the pot odds
over two streets, if I got the draw already on the flop.
Implied odds I am trying to factor in as well. It might be that the chips I have to add to the pot is more than 20 % of that pot, but if I reckon villain will bet (or call) again after I hit my flush then the return payment will be more in my favour after that.
For example before the river the pot may be 4000 chips and villain bets 2000 chips. I would have to pay 2000 chips which is 25 %, more than the odds for a flush. But if I hit the flush then villain will give me another 2000 or 3000 chips as a bonus.
Maybe someone can tell if this is completely wrong.