That's the point though - they were very few in number, very unstable in their control, and none which lasted either the duration of the war or in any place so long as the confederates thought it was worthwhile to remove them. Most of them consisted of a small landing party somewhere along the coast that either occupied an area and then left it behind to be easily retaken when they moved up the coast or got pushed out to sea entirely (as happened when the occupied Galveston).
As for the orders you post purporting to come from Fort Bliss near El Paso, they are the apparent product of an isolated outpost that the californians occupied during the second half of the war after the confederates left the place for want of any use since it was out in the middle of nowhere. Yankee indian patrols were stationed in Fort Bliss at the war's outset but they retreated from it into New Mexico in 1861 as Baylor with volunteers to relieve the city of Mesilla (the capital of southern new mexico, which was confederate in sympathy but was under union occupation). Fort Bliss was used by the confederates from then through the summer of 1862 as a supply base for various operations and skirmishing in the New Mexico-Arizona-Colorado region. It was reduced to rubble when the confederates abandoned it for lack of any need. Carleton and a tiny calvalry band looks to have arrived a few months later, set up camp nearby at an old mill site, and spent the rest of the war fighting apaches with virtually no coordination over much of anything from Washington. Juarez popped up there for a brief period while hiding from the european forces. The confederates appear to have simply ignored him for most of the remainder of the war because he wasn't doing anything and in fact really couldn't do much of anything, being stuck out in the middle of nowhere.
Texas was a backwater in the ACW. Especially west Texas. The best troops had been sent east with Hood and Robertson, et al., and there were few strategic objectives to be had.
The capture of Fort (Jefferson) Davis in August 1862 had great symbolic value, however, even though it was just a few, mostly ramshackle adobe buildings.
As you could see in the previous post with the OR citations, the Union and rebel forces were somewhat more concerned about the Indians than each other, and when the rebel POWs were paroled to San Antonio, they were escorted for their own safety.
Your story about the confederates abandoning the Rio Grande forts "for lack of any need" not jibe with leaving their sick and wounded behind. Those, from several outposts, numbered over 100. It sounds to me like the able-bodied Texans quickly skedaddled.