Depends on your adhesive material.
Using a Qwikset type product? use the dimpled side UP, apply a thin layer of cement with the flat edge of the trowel, then spread the adhesive amount of material with the square teeth.
Using a Mastic type product? use the flat side UP. Mastic is not recommended for heavy traffic or heavy water.
I personally recommend a qwikset with that type of subflooring.