For the best finish, take the toilet and pedestal out.
Depending on the size of the bathroom, you may need to section the plywood. But make sure your cuts fall onto the centre of a joist (just like plasterboarding), so that you can secure them down correctly.
Screw down at 300mm centres and make sure you leave a mil or 2 gap between sheets to allow for expansion.
Then before you tile, seal with acrylic primer 🙂