Should we assume that the top of the foundation of our building would begin at ground level or would considering a parking garage/basement/storage area be allowed below the ground level which would permit the top of our foundation to be at a lower depth? From my understanding the majority of structures like ours would have some sort of subterranean structure like I described.

Architecturally you can include anything you deem necessary, including garages or basements, but the structural model should just represent the structure above ground.