Many times the stock cars were already at the siding where the pens/chute was located. Using the D&RGW or AT&SF, shipper would request to load on a certain day, around a specified time as set by the railroad.
The stock usually arrived the evening/afternoon before, was given feed/water. Cowboys or Sheep Herders camped overnight and were ready to load when the locomotive & train crew arrived.
In the late 50's I watched sheep being loaded at Farmington, NM. Engine #488 was used to move the cars up at the chute when one was completed. Before sunset all was completed and the train headed for Durango, then on to Chama & Alamosa. Probably at Alamosa the sheep were unloaded and given feed/water. Next loaded into standard gauge cars for the journey to Denver or Eastern Markets.
It is very hard to load sheep at night, they will not move up the ramp into the upper or lower car deck. Sometimes their is a "lead sheep" that goes up the ramp & all other follow. This "lead sheep" will come back down the ramp after all the following ones are inside. Next it will be used to herd another group up into the car.
There is a Federal Law that live stock must receive feed, water, and rest after so many hours in transit