I have tried both ways.
Doing the bottom first means you wont see gaps when looking down at the tray, plus what Todd says, doing the sides first means the bottom has to be perfect to ensure you don't have any gaps around the edges in the tray that can be see at first glance.
Doing the sides first give you more room for mistakes that can be covered with padding and turf as you build up the tray, for example around the rear of the tray where the gunwales meet with the flat surface of the tray. It is nice to be able to have the bottom layer of turf over lap in this area for a cleaner look. You also wont have to fight tight spaces within the footholds when trying to wrap the footholds properly, a turfed tray will give you less room to work in such a tight and tough space to perfect.