Well the specific answer to the particle change question is that you can drag a media file from the File Browser or Library, then drop it into the Media tab, then drag the object to the "Bat" Particle Cell>Particle Source Well and it will replace the Bat movie with whatever you want. It's a good feature of Motion that you can tweak the presets for your own needs.
Also, there are bird presets in Content>Fauna>Bird & Birds 01. The "Birds 01" is a bird flock particle emitter, which may be what you're looking for, or maybe not. You might have to create your own animated particle cell (or even roto footage of a real bird in flight with Motion's masks, etc.). You could then use some of the Simulation Behaviors (Align to Motion, Attracted To, Drag, Random Motion, Wind) maybe in conjuction with another transparent ("null") object to control your "flock."