Mechanical media at the bottom and bio media at the top is how I do it. On my Sunsun 302 I run several layers of sponge in the bottom tray, plastic pot scrubbers in the middle and various bio media in the top (302 is only a 3-tray).
On my Marineland C360, layers of sponge in the bottom two trays and bio media in the top two.
I don't run any type of chemical media like carbon or purigen, but if you wanted to run those, they go up top as well.