Dark checking to the aggressor on the flop might seem unusual, but many players check 100 percent of their hands OOP to the pre-flop raiser. For those types of players, dark checking is literally no different than waiting to see the flop and then checking.
A dark-check on turns and rivers needs to met with more thought, but not necessarily more thought than a simple standard check on those streets. However your proceed, make sure you are balancing your range with your best hands and your worst hands that either block some of his value hands (like, say, those with an Ace in them), or those that don’t block his bluff combos. Also, you should be polarizing your range even further on rivers when facing a check.
In general, the best players typically don’t dark check on turns and rivers. I find it mainly to be more a tactic of recs who are trying to get cute in some way. Don’t let one or two bad experiences with this move frustrate you. Always try to think about what are the best hands you will have, and what are the worst hands you could have, and balance your action based on that.