Fit the backer boards after fitting the tray. This, when boarded and tiled, will make the tray look nice amd low. You can fit most trays with tile adhesive ( I do) powdered flexi. Put Silicon on the edges that go against the wall. Make sure you prime the floor and back of tray. Only use Silicon to stick down if the floor and tray are perfectly flat.
When fitting the backer boards, keep them a few mm from the tray and fill the gap with Silicon. This will stop the boards from squeaking! When there is any movement. ( there should be none! But do it anyway)