See, this is what happens when you assume
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Try the map below, from the May 1978 RAILFAN.
The black (AT&SF) line to the north is the southbound main of the Joint Line. The red (D&RGW) line to the north is the northbound main of the Joint Line. The red line to the west is the Royal Gorge / Salida / Tennessee Pass line. The red line to the south goes to Walsenburg / Alamosa / Trinidad.
Yes - Train no. 1 in the photos is actually pointed compass northwest when stopped at the depot, even thought it was "southbound" until arriving Pueblo. Train no. 2 departed to compass southeast, turned east, and eventually north.
Finally, go back to the Terraserver link and you can now pick out the wye no. 1 would have used.
[terraserver-usa.com]
Depending on whether the train arrived from Denver on the AT&SF trackage or the D&RGW trackage, it would approach Pueblo Union Depot from the opposite direction. (In other words, it's physically possible, though bloody unlikely, that two sections of the same southbound train could enter the station in opposing directions, because one came into town on the Santa Fe, and the other arrived on the D&RGW.)
JAC