Victor Moses and Mame Biram Diouf scored the goals at the Britannia Stadium to sink Everton.
Stoke have now won three on the bounce in the league to give boss Hughes cause for celebration.
"We're doing fine, we're ahead of where we expected to be in the league table," said Hughes.
"We're eighth at the moment and we'd love to finish the season in that position."
The only negative for Stoke on Wednesday came when defender Philipp Wollscheid suffered with a groin injury and was hauled off after 17 minutes.
Hughes said: "We had to overcome the disappointment of losing Philipp in the opening minutes – he felt his groin in the warm-up.
"He gave it a go but he'd lost power in his left leg and in the end we had to take him off pretty quick.
"Geoff [Cameron] came in and did well and we didn't left that effect what we wanted to do and in the end deserved the victory."
Moses netted his third league goal of the season and Hughes added: "It was a great opening goal by Victor Moses who I thought was excellent. He looked really powerful and strong right to the end, as they all did.
"We always looked dangerous on the counter attack and, in the end, got the second goal which took the game away from them.
"I'm really delighted to win three games in a row."
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