Three goals in just 202 first-half seconds from Maynor Figueroa, Callum McManaman and Jordi Gomez stunned the Toffees, who were looking for back-to-back semi-final appearances.
"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."