We are replacing a toilet and putting on overlay of wood and lanoliem. How do we make the toilet fit onto the excisting flange?

You piggybacked onto a dead thread so I gave you one of your very own.
Put the floor down around the flange, Then. When you're ready to set the toilet purchase a set of flange extenders (see image)and you're all set. Good luck, Tom

How thick is your flooring material and the plywood?