DOBO leaves Dover and comes down the Freight Mainline to CPW-WJ (or Wilmington Jct). So, yes, they pass through Rockingham Jct, Newfields, Exeter, Plaistow, Lawrence, Andover, etc.
At Wilmington Jct, they come down the Wildcat Branch to Wilmington, then into Somerville on the New Hampshire Route mainline (Lowell main). They enter former Yard 8 at the handthrow Walnut Street crossovers. Normally, they would come in at Somerville Jct, but Guilford hasn't bothered to fix the 4th Iron between there and Walnut Street since derailment damage back in 12/01. DOBO will meander down through old Yard 8, ending up behind the MBTA's Boston Engine Terminal. At FX (near Sullivan Square),
they'll work BS&G. BODO goes the reverse route.
DOBO/BODO can operated via Reading (Western Route mainline) between CPW-WJ and Reading Jct (Sullivan Square), but this is rarely done and only allowed in emergencies.
Those cars you saw weren't empties....all still loaded as of Sunday afternoon. Also of note is the last car on the BET end of the cut: a SOO LINE 4 bay hopper with some sort of speciality mineral load. These come into Somerville via LOSA.
DOBO averages 25-35 cars of late. Not like the heady days of the Big Dig era when the Everett facility was open and DOBO ran with 40-60 cars.
Dave