Do I run screws through the "tops" or through the "bottoms" of the corrugated steel in roofing?
A

If you choose B you will dimple the steel, ruining the look while creating a penetration point for water because expansion and contraction of the metal due to heating and cooling will create an open access point for water to enter, and a big opening behind it to receive it.

A, however, will give you a tight seal against the wood, wood-steel-screw in a nice tight sandwich - resisting expansion/contraction gaps and thus protecting much more effectively against water penetration while preserving the look of the corrugated steel