Yeah, this one might warrant some explanation.
Remember, Doctor B stayed in the future. Marty disposed of the Flux Capacitor from Delorean A. Aaron took Delorean A to the store and inexplicably time traveled. They hit the killer with Delorean A. Aaron gets stabbed. Doctor B arrives in Delorean B and incapacitates the killer. Doctor B sends Aaron and Marty to the future in Delorean B leaving Delorean A on the side of the road in the present.
Confused yet?
Good.