I'm new to this and I can't figure out why all my exported animations in Unreal Engine are face down on the floor. Everything else works fine but I can't get them upright. Is this an issue with my export settings that I am missing or is it something in Unreal?

UE and Mocap Studio use different coordinate systems - directions of coordinate axes differ. Thus you need to apply a coordinate transform when exporting for UE. There are control for changing the orientation of coordinate axes on the Export tab.
Try using "UE Mannequin Rig" from the Target character dropdown. It already includes the correct orientation.