Duran hit a screamer to settle the 3-2 win for the hosts on Saturday.
Emery later said: "Yes, but he came back on Friday and only did one training with us after he played with his national team. He’s made a good impact in the last three matches we played, scoring goals and helping the team. For this reason, he was playing in the starting 11 with Colombia.
"He’s in a process, but of course his potential is huge. I want to get the best of him, support him, be demanding with him. And then, he’s possibility getting better, building confidence and scoring goals. Today he scored one goal but he had another two chances to score.
"But today, Watkins scored two goals. I think it’s very good, we have to feel comfortable with those strikers and as well feel proud of how we can play with two strikers. We are playing one, playing both. This is the challenge we have."
On Duran's unpredictability, Emery also said: "Of course, we are very demanding in our structure and how we want to play, being organised. But we need the skills and the individual players doing something special sometimes. Football is always like that and it’s not going to change.
"We want to be organised but as well it’s for the players. Duran did it before, he started playing two years ago. At Manchester City away, he shot like he did today - crossbar. He scored last year against Liverpool here shooting outside the box, he scored against Ajax with a shot like that.
"When he’s shooting, of course, we are giving him confidence to do it. Sometimes he will score, sometimes he will not but he has the capacity to score from there because he has a very good shot. He has potential to exploit with us here a lot of things more tactically and with the connection with the players.
"The summer was a little bit strange and not clear. But when we decided and he decided with us to stay here, we started again the process. I am happy and like you know, we believe in his potential."