The Potters recorded their third-straight victory for the first time this season, allowing them to move up to eighth on the Premier League table, courtesy of goals from Victor Moses and Miame Biram Diouf.
However, it was down back where Stoke were most impressive after losing German defender Philipp Wollscheid to injury in the 15th minute, forcing a reshuffle.
"We had to rejig the back four once again which has been the story of our season," Hughes told Sky Sports.
"But once again the group of players didn't allow that to affect them. We've done that time and time again this year we've just picked ourselves up when things have gone astray.
"We've done tremendously and on the night, we just kept at it. Everton had a little bit if possession but they never created anything of real note.
"We defended really well and Victor Moses scored a fantastic header. Then we were in a position to soak up pressure and hit them on the break.
"We made a couple of changes which allowed us to hit on the counter and in the end we got the second as a result of that so all in all it's a fantastic period that we are in at the moment."
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