I doubt that Second Nationals were used at Chickamauga for anything other than HQ flags.
The only use of Second National battle flags for Western units that I can find are these:
1) Some units of Forrest's Cavalry Corps issued in the Spring of 1864. These include the 7th TN Cavalry and the 18th Mississippi Cavalry Battalion (which was captured at Brice's Crossroads). I doubt that most of Forrest's units did not have these flags and they were issued to only some of the units as they were homemade. These were also before his corps got the 12 star Mobile Depot flags in July, 1864.
2) The regiments of Loring's Division which came in December, 1863.
3) The presentation Second National flags to Gibson's Louisiana Brigade and some Alabama units. Also made in Mobile, these only had 12 stars.
Other than these, I cannot recall any combat use of Second National flags in the west.