Goals from Kevin Lisbie and Clive Platt in the opening 15 minutes ended a run of three league games without a win for Colchester and inflicted on Stockport their sixth successive defeat.
But Boothroyd said: "It was a case of job done. We didn't do it in a great manner, but it was a professional performance.
"We were terrific in the first half an hour and I was pleased with that. In an ideal world, we would have kept pushing for more goals.
"The fans want us to play like Brazil and I'd like that too. But you're not going to play well in every minute of every game during the course of the season. We're a work in progress and the sign of a winning team is when you are able to dig out results."