Collingwood recorded its fourth win and highest score of the season in Sunday's victory over Gold Coast.
"I'm really proud of our performance, you don't see what goes on behind the scenes," Fly said post-match.
"This week we have been scrambling to find what our best team will look like, we have a lot of injuries and illness.
"We're missing half a dozen - including a couple of coaches.
"We test every day for Covid but the man flu can be terrible for some."
With another new-look forward line, 10 individual goal kickers contributed to the season-high 115 points.
"I've said this every week but our forward line has looked different in every single game," Fly said.
"We would love to get some continuity but we have a system in place and the system is working."
Debutant Aiden Begg and Darcy Cameron rotated through the ruck in the absence of Brodie Grundy.
"I'm really proud of Darcy, he was competing really hard all day," McRae said.
"We're looking at three months without Brodie so the ruck combination is a work in progress but I was really pleased with Cameron and Begg.
"They both played their role really well."
Cal Brown was a late in, with Reef McInnes becoming emergency sub.
"We moved him (Brown) out, thinking he wasn't going to be right but all of a sudden he was available," Fly explained.
"He was sick and he did really well to get up, the message we had from the doctors was that he wasn't likely."
Josh Daicos was superb on the wing - kicking two goals from 20 disposals - and McRae praised his work ethic.
"Josh is doing a lot right, he's attacking the ball and using it well," he said.
"He's working hard and getting the best out of himself and playing good footy for the team."
Fly was reticent about his intel from Tigerland ahead of next week's match against Richmond.
"I'm glad Dusty is back, that's awesome," he said - tongue firmly in cheek.
"I have great respect for Richmond and there's a a lot of people there I love.
"We have a job to do, we know their strengths and we will give it our best shot."
