I do know that you need to get a catflap that is suitable for glass really. I had a catflap installed in my playhouse and I was told that if you get one meant for normal doors, it will be too thick for your wood.
Because glass is thinner, the two panels of the catflap should fit together properly on one meant for glass.
My grandad did mine for me, but I think you get a cutout of the catflap and draw it onto the hutch/shed, so you can see where to cut on both sides. I wouldn't have been able to do it, it was really hard getting the screws to stay in through both sides of the catflap, but I'm not DIY savvy at all! I think he did use an electric saw though.