Wells said his team set out "to dominate up front, minimise mistakes and play the game in the right area of the field" against Otamatea, who were coming in hot after a tight win against Old Boys Marist in the previous round.
Otamatea coach Dean Kenny said a lack of accuracy let his side down.
"In the first half we tried to play an expansive game too soon. A couple of unforced errors there allowed [Waipu] to turn them into points."
The loss of Super Rugby player Matt Moulds was hard on Otamatea.
"He's stabilised a lot of our efforts," Kenny said of Moulds' influence as captain. "In saying that, we had our opportunities."
Waipu flyhalf Ben Mathers played a commanding role at pivot to outshine Otamatea's Dan Hawkins at times.
"He's classy all right," Wells said of Mathers. With a backline starting to fire, a late resurgence could be on the cards for Waipu.
"Our backs hadn't really clicked into gear so far this year but I think they took a big step forward."