Three goals in four first-half minutes from Maynor Figueroa, Callum McManaman and Jordi Gomez stunned the Toffees, who were looking for back-to-back semi-final appearances.
Martinez has consistently said staying in the top flight must always be the Latics' focus, fielding weaker sides in knockout competitions with four changes for Goodison Park, and no trip to Wembley would deflect that.
"I have said time after time I've made eight or nine changes in the past (in the cup) and since I have arrived at Wigan we want cup success, but not at the expense of the league form," said the Spaniard.
"Making nine or 10 changes is a need in the modern game. The difference now is this season we have a group of 24 players who have shown when they get the opportunity they are competitive.
"If anything this cup run has given us extra players. I think Callum McManaman showed he is ready to play in the league and (goalkeeper) Joel Robles showed a great level of performance.
"This cup success is bringing extra competition into the league campaign and that is what we need to get from this success."
For all the criticism of Everton's poor showing Martinez was adamant his side were worthy winners.
"I think you have to be at your very best at Goodison Park to keep a clean sheet," the Wigan boss added.
"We played well but more importantly we had incredible concentration levels.
"To score three goals away from home in the manner we have done we always looked a real threat going forward and it was a complete performance and a special day for Wigan.
"You unfortunately get used to people saying if you lose it is because you are Wigan and if you win it is because the opposition was poor.
"They weren't poor. My players deserve credit for how they stopped Everton. We stopped the full-backs going forward and getting crosses in from dangerous positions.
"Attacking we kept the ball and I don't think they gave us anything for us to score three so it is unfair to say Everton had a bad day.
"In the second half they threw everything at us and we coped very well.
"It is more a day of a very good performance from our point of view and a well-deserved semi-final."