This is a perennial topic, but here it comes again. East of Rensselaer and west of Buffalo, the four track segments were operated right-handed, with 1 and 2 in the middle and 3 and 4 on the outside. They were numbered from the south 4-2-1-3. Tracks 1 and 2 were the "high speed" passenger tracks, and 3 and 4 were freight and local passenger tracks. In the NYC system of track numbering, sidings and yard tracks in those territories were numbered consecutively away from the mains, with 6-8-10-> on the south, and 5-7-9-> on the north.
Between Rensselaer and Buffalo, the two passenger main tracks were 2-1 on the south side, and the freight main tracks were 3-4 on the north, numbered south to north 2-1-3-4. The reason for this was to keep the freight yards on the north side, and the passenger stations on the south side; and to avoid as much as possible the meeting of freight and passenger trains running in opposite directions, in case of a derailment or an over-wide load. The freight tracks were operated left-handed and the passenger tracks were right-handed, so the two middle tracks 1-3 were westward, and the two outside tracks 2-4 were eastward.
Dewitt was a left-hand yard, with the eastbound hump on the north side. Selkirk was a right-hand yard, with the eastbound hump on the south side. The passenger bridge (Maiden Lane) at Albany had passenger tracks 2 and 1, right handed, and the freight bridge (Livingston Ave) had freight tracks 3 and 4, left-handed.
When Selkirk Yard was built, along with the Hudson River Connecting Railroad, the freight operations east of Selkirk were essentially double track railroads with right-hand operation (River, Hudson and B&A). They needed a way to swap "handedness" with a minimum of traffic conflict, so they built the flyover bridge at Fullers Crossing where the West Shore crosses US Route 20, Western Turnpike. Thus the West Shore (now Selkirk Branch) trains could leave Dewitt running left handed, then become right handed at Fullers and enter the proper side of Selkirk.