Town ran out 2-0 winners with goals from Roy O’Donovan and Luke Guttridge to consign the Bees to relegation from the Football League and finish sixth in npower League Two.
They will now face Cheltenham Town over two legs, the first of which will be at Sixfields on Thursday night and the second at Whaddon Road on Sunday evening.
Boothroyd says he must make the most of a full-strength squad for those games, a luxury he is afforded after club captain Kelvin Langmead, Clive Platt, Joe Widdowson and Ishmel Demontagnac all sat out Saturday’s game.
“The first half wasn’t particularly good and sometimes you get that when you change the team around a little bit,” he said.
“When we got up the pitch in the second half it enabled us to keep hold of the ball a little bit better and we could have had a couple more goals.
“We knew we would finish in the play-offs and I want to have everybody 100 per cent fit for the big games we’ve got coming up.
“It gives everybody an opportunity to stake a claim and to put themselves forward. I’ll have lots of players available for training on Thursday night.
“We’ll have more or less a full squad available and we need to make sure we make the most of that. I’ve got some really nice problems.”
Boothroyd commented prior to the match that the 4-0 loss to Barnet in October is the result that has upset him the most since he has been Northampton manager but some revenge was administered for that result on Saturday.
As well as ending a five-game winless streak and generating some momentum for the play-offs, Town’s 2-0 win also consigned the Bees to relegation, a fate which hung over Northampton for long spells of last season.
“That was us last year,” said Boothroyd. “It was very stressful for us but this time we’ve finished a good few points better off.
“I think we’ve got what we have deserved this season. It’s been a long season, we’ve had some brilliant performances and some rubbish performances, and Barnet away was one of those.”