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.

Can we have different uses in the zones? for example can floor 3 be residential but floor 4 be commercial (restaurant or office)?

Yes

My team and I are wondering if we can use the site given in the ground motion as our site location or do we need find a different one. Thank you and hope to hear from you soon.

Please use the same site (4th and James). This site corresponds to the location where the boring logs were obtained and is the assumed location of the building.