Trouble Exporting Video w/ Alpha Channel Into Media Encoder

Fellow Editors,

Need a way to streamline our keying workflow.

Currently rending/exporting clips with alpha channels in Premiere and After Effects takes too long. We need to be able to render/export in the background (through Media Encoder) so we can keep editing and hit our deadline each day; however, we can't seem to find an export setting that allows the clips to be rendered in Media Encoder with an alpha channel.

Any suggestions?

Working in Mac OS.

Thanks,

Logan