I often design metal deck by applying the design loads, to a simple or single-span condition, to determine the required Sx and then choose the deck based on the given Sx/Sp/Sn of the proprietary, SDI endorsed load chart and/or section properties. Simple span is certainly conservative, but, for simplicity, it satisfies most of my concerns.
You should design the metal deck for all applicable conditions. If you have simple-span conditions, then "Yes", design it for simple-span.
The contract documents should provide an explicit framing plan that would show all span conditions for the metal deck to be furnished.
If you feel that either your spec book or your General Structural Notes sheet does not provide sufficient information to draw necessary attention to what you want understood, i will often provide an additional note or specification within a box, near enough to the framing plan to clarify a special condition.
Is there something else you wish to convey that i may not have covered?