My reply assumes you'd want to depict units actually serving in the Trans-Mississippi. If so, I think it depends on which state's forces you want to depict, and when.
Frederick Adolphus documents the use of federal "Old Army" clothing by a Texas unit in the first half of 1863 (and maybe a little later) here:
PDF link
The article does a good job documenting the ratio of federal to other clothing, as you can see. Extrapolating from that, you could argue that Texas units supplied from captured San Antonio stocks likely wore similar ratios of federal clothing in 1862-63. Adolphus' article suggests that stopped from mid- to late-1863.
I'd argue that Louisiana and Arkansas troops – and Missouri units in Arkansas, as well as Texas troops not supplied from San Antonio – would not have had much, if any, captured federal clothing, at least up to the summer of 1863. They simply hadn't won any battles, or captured any federal supplies, to put them in a position of having federal clothing on hand.
In the late spring/summer of 1863, the units serving with Taylor in his demonstrations in southern Louisiana did capture federal clothing. Blessington, a Texas soldier, wrote in his post-war "The Campaigns of Walker's Texas Division" (p. 133): "[W]e met Mouton's Division of Louisiana troops, who were nearly all dressed in Federal uniforms that they had captured" in one of the battle's of Taylor's campaign. Further, Confederate forces in Louisiana in the fall of 1863 did win a few actions, so that those troops – Louisianan and Texan – perhaps would've had access to captured clothing.
Guerillas, and troops in the Indian territory, are another story.