Stoke have taken seven points from their opening five Premier League games, as well as beating Walsall in the Capital One Cup, since Hughes took charge in the summer.
Hughes feels things are going well but he has stressed his Stoke side are "still very much a work in progress" as he attempts to evolve their playing style after replacing Tony Pulis.
"The more games we can play, the better for the group in terms of what we are trying to do," Hughes said when asked about the trip to Tranmere, who are another third-tier team.
"At this point in the season, we are still very much a work in progress, so games will help us. We will get better as we play more often together.
"I feel we have taken huge strides in a small space of time but we need to keep the performance levels going in the right direction.
"After a difficult opening period, where we have played Liverpool, Manchester City and now Arsenal, I think we have come through that in good heart and with a lot more confidence, so we are in decent shape."
After vowing to name a "strong" side for the Walsall game, Hughes made eight adjustments to his starting line-up and the Potters first XI looks set for another considerable reshuffle on Wednesday night.
"I am looking to give some game time to players who were not involved against Arsenal, and there will be an opportunity to do that," Hughes said.
"However, we are still looking to progress in the competition - it is one which we feel we can do well in this year."