After Shaun Wright-Phillips' opener, Wayne Rooney scored his first competitive goal for England in more than three years, then an own goal from Taavi Rahn completing the scoring after 34 minutes.
"Then it was a case of 'we've won that game', make a few changes and look at one or two things and make sure we're right for Wednesday," said McClaren.
"We didn't perform well in the second half, I can understand it will be flat, we're going to be thinking about Wednesday.
"I can't criticise it - I watched Croatia play Estonia and go 2-0 up and stroll the second half to conserve the energy. That's what we did."
Man-of-the-match Gareth Barry maintained the hard work still lies ahead.
He said: "It is a great feeling to be named man of the match here at Wembley on the back of a great team performance and victory.
"Things are looking good at the moment but we know it is only half a job done because there is another big game - probably the biggest for a long while - coming up in Russia.
"The Russians have to win the game and so we have to go there and be positive to get the three points.
Rooney added: "We have got the job done today and we've got a similar game in Russia to the one we had to tackle in Istanbul a few years ago.
"We know it will be difficult and it will be a tough game - but we've got to go out there and attempt to do the job we know we have to do.
"It was a nervy night over there in Turkey. We had a few chances and could have won it. But we went out there and did a job and I am confident we can do the same again.
"There is definitely the belief and quality in this squad to get the same sort of result. There are a few younger players in the squad now - but the same, if not more, quality."