The Gunners picked up a deserved 2-0 victory at the Emirates Stadium as an Aaron Ramsey strike and a Kalidou Koulibaly own goal put them in charge of the tie.
Emery admitted on the eve of the tie that his side needed to win at home, given their poor form on the road this season.
They have lost both away knockout ties in this season's Europa League to BATE Borisov and Rennes, two teams not considered as strong as Napoli - who sit second in Serie A.
Coupled with a return of just five Premier League away wins so far under Emery, the Spaniard feels their place in the semi-final cannot be taken for granted quite yet.
"It's 50-50," he replied when asked how he saw the tie after winning the first leg.
"The result doesn't change the idea I had before the match. It's 50/50 - the result is a good result and can give us some advantage, but playing away, I know continuing with the same 50/50 for each team.
"I think it's a good result but we know it's going to be very difficult because our performances at home have usually been very strong.
"They're going to use their possibilities and attacking options against us for a comeback. Our objective now is to continue being competitive like we are here, away with our gameplay for the next matches.
"I think we deserved the result. The two halves were very different because in the first half we controlled the ball very well and controlled with our positioning and attacked their box with the players, scoring two goals and some chances more.
"We didn't concede a lot for them, only the one chance they earned in the first half."
Napoli coach Carlo Ancelotti was at a loss as to why his side started the game so slowly but believes if they can replicate their improved second-half display at the San Paolo Stadium there is still a chance to progress.
"I was surprised by the lack of courage and personality from my players initially," he said.
"We had worked on this. Turning things around now will be difficult, but we'll be home, at the San Paolo, and the fans will help us.
"In the second half we managed to do better, create chances, so I have hope for the second leg. It's difficult, not impossible."
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