I sometimes watch Nakamura's video and see Nakamura used to say "It's just winning," even though he got the same materials as his opponent. How do I know which positions are winning? And how can I make those positions?
Yes, just spend your life studying chess and it will all become clear.
Nakamura is a genius and one of the top GMs in the world. When he says, "It's just winning," he's relying on thousands of hours of study, experience, and play. We mere mortals are not supposed to see "winning" in the same positions that he sees it in. When I say, "It's just winning," I mean that I'm ahead by a queen and a rook and my opponent has 10 seconds left on his clock to my 30 minutes.
From my understanding, recognizing winning positions are determined by comprehension positional chess. Sounds stupid, I know, but to be more explicit. Factors in determining winning positions are king safety, pawn structure, mobility of minor pieces (open files, ranks and diagonals), control of key squares (usually the center).
Some might disagree with me, but I suspect improving our endgame will actually improve the comprehension and creation of winning positions.
When I say, "It's just winning," I mean that I'm ahead by a queen and a rook and my opponent has 10 seconds left on his clock to my 30 minutes.
ROFL! 
@AkiraSaga + 1. My impression from annotated GM games is that if a strong player looks at a position and sees, for example, white has two potential outposts and a good bishop whereas black has no weak squares in their favour, a bad bishop, and a weak pawn, then they would declare it winning for white. They are looking objectively at which side has the greater positional (long term) strengths/advantages or fewer weaknesses that they can build a plan around. Whether the 'winning' side actually wins then comes down to converting those advantages vs how well the opponent can mount a defense.
I sometimes watch Nakamura's video and see Nakamura used to say "It's just winning," even though he got the same materials as his opponent. How do I know which positions are winning? And how can I make those positions?
First of all, if you could evaluate the same position on the board like a super GM, you would be one. So it is completely natural that he sees that it's a winning position while we... do not.
That being said, besides material, there are many things that could decide the position: piece activity, weak squares aka potential outposts, passed pawns, king security, a lot of space opposed to cramped position etc. So basically he sees the board, evaluate these things I've mentioned and some more things, and based on his vast experience he knows which side is better and roughly by how much.
I sometimes watch Nakamura's video and see Nakamura used to say "It's just winning," even though he got the same materials as his opponent. How do I know which positions are winning? And how can I make those positions?