The VRE trains run in a push-pull configuration; they go backward on inbound runs and forward on outbound runs. They hold the trains at three yards at either end of the line -- in D.C., the yard in question is the Amtrak facility at Ivy City, and serves both lines. In Manassas, there's a small yard just past the Broad Run/Airport station; on the Fredericksburg line, VRE uses the Crossroads yard just south of Fredericksburg station.
Also, VRE now goes to Richmond, sort of, using a bus bridge provided by the GRTC Transit System. Actual rail service to Richmond is still years off, though.