How do you tell if this sentence DujlIj yIvoq means 'Trust your instincts.' or 'Trust your ship.'?
Context.
It's the same as telling the difference between English words that sound the same. Does "He lies" mean "He tells a fib" or "he reclines horizontally"? Is a "bow" a thing tied from ribbon, a thing you do with your waist, the front of a boat, or a thing you shoot arrows with? All of this is determined by context.
So, if they are talking about ships, then {DujlIj yIvoq} will means "Trust your ship", while if they are talking about instincts it will mean "Trust your instincts". The reason that it can mean both is part of Klingon culture, to Kingons trusting one's ship is like trusting your instincts (and vice versa).