I found your previous discussion with Mr. Coffee from this forum. I take it you are still of the opinion that the battle field was several miles north and west of the marker and confederate cemetery. I gather Geary's station is now underwater (Atoka resevoir/lake). The best period map of the area I've found is: http://www.civilwaralbum.com/atoka/map1.htm
A very helpful guide to understanding the route of the Butterfield stage is found at http://digital.library.okstate.edu/Chronicles/v035/v035p055.pdf This helped me get the names of the times squared away.
There is a foot note reference to a map I'd love to see.
"15 Wright, op. cit., p. 822. The route of the Butterfield Overland Mail stages in Southeastern Oklahoma along the old road from Fort Smith to Red River is shown on the map that accompanies this article (1957). Approximate routes of
other trails in this region are shown to aid as illustrations, many of them important in Oklahoma history"
Taking what was previously mentioned and my very limited geographical knowledge of the area; I get this layout. From Colbert's Ferry going east, 13 miles to Fishers Station, 14 mile to Nail's, 17 miles to BOGGY DEPOT, continuing east 16 miles then to Geary's Station, then 15 miles to Waddell's Station. (Waddell's is often confused with Rogers a post war station that replaced Waddell's about 3 miles further east.) Then on about 16 miles to Blackburn's
Modern markers are as follows:
Blackburn's: North of Pine Top School in sections Four and Five, Township Two North, Range Fifteen East, Pittsburg County.
Waddell's: On county road three miles west of Wesley, Atoka County.
Geary's: Inundated by Atoka Reservoir, about one and one-half miles southwest of Stringtown, Atoka County.
Boggy Depot: Four miles south of State Highway 7 bridge on Clear Boggy River, in Boggy Depot Park, Atoka County.
Nail's: East side of Blue River, about two miles southwest of Kenefic, Bryan County.
Fisher's: Two miles south of U.S. Highway 70 and four miles west of Durant, Bryan County.
Colbert's Ferry: On grounds of the old B.F. Colbert home site and near grave, about one and one-half miles southeast of Colbert, Bryan County.
BOGGY DEPOT also sat on the old military trail from Fort Smith, westward, to Fort Washita and Fort Arbuckle. I believe this may be a distinctly different trail than the Butterfield Line Road (which closely followed the 1837 Indian migration trail.)The best description of the Civil War era Boggy Depot is Muriel Wrights" 1927 article : http://digital.library.okstate.edu/chronicles/v005/v005p004.html
This area had been extensivley surveyed prior to the war ( http://digital.library.okstate.edu/chronicles/v005/v005p333.html#fn10 ) including Whipples expedition for the railroad. The trails were well marked and used by 1864 with a good deal of war commerce transiting the area.
From Wright again "-The regular session of the Choctaw General Council held its regular session in October  at Boggy Depot, the capital of the Choctaw Nation, with Tandy Walker as Governor, when special legislative acts were passed and approved, providing for improvements on the public road from Fort Smith through the Nation and granting tollgate privileges for building and maintaining such improvements. Some of this work had already been done during the summer undoubtedly through arrangements by the Butterfield agents. There were six of these acts granting to certain citizens the privilege of making improvements on the road and of operating tollgates: Washington McDaniel and Charles M. James, a bridge and tollgate near their residence on Brazil Creek, about twelve miles
southwest of Skullyville ; William Holloway, a turnpike and tollgate at "The Narrows" just west of his place of residence near upper Brazil Creek, (Holloway's Station) ; Captain John Riddle, a bridge and tollgate on Fourche Maline Stream, near his residence (Riddle's Station) ; A. W. Geary, a bridge and tollgate on North (Little)Boggy, (Geary's Station) ; James D. Davis, a bridge and tollgate
on Muddy (Middle) Boggy, about five miles south of Geary's; the heirs of the late William Guy, a bridge and tollgate at their mill on Clear Boggy River, about a mile east of Boggy Depot where they maintained the Overland Stage station.
The Rock academy I presume is not the Wapanucka(present day Wapanucka) Academy located on Wapanucka or Delaware Creek 12 miles Northwest of Boggy Depot,(see map, I think Rock Academy is the one marked closer to Shawnee Town and the mouth of the Little River) so named because some Delaware Indians lived on the ridges along this creek, years before the Civil War. From Wright again " This creek was at that time often erroneously called Delaware Creek; it was really the west branch of Boggy River which divided into two streams, about six miles west of north of Boggy Depot, forming what was then called "The Island." The two branches joined again south of Captain LeFlore’s bridge (built 1866) which was over the east branch. The mouth of Delaware Creek empties; into the main streams of Boggy River, some distance above the north end of "The Island." The Fort Smith road passed over the lower end of "The Island," thus crossing the two branches of Boggy about 100 yards above their confluence. The River is a fickle stream for when Captain LeFlore built his bridge in 1866, its east branch, in this vicinity, was the larger, but when the flour mill was built the west branch carried the most water; to-day the main body of water flows through what was a dry slough, leaving the mill dam in a deep, almost waterless channel to the west.
Further I believe that Phillips description of "____Courthouse" is a reference to Boggy Depot ala "in July, 1861, the Choctaw and Chickasaw nations were constituted a judicial district of the Confederate states, called the Tuskahoma District, Boggy Depot being designated as the court town. "
Looking back at the map I referenced at the beginning of this tome I think I come to the conclusion that Phillips marched Southward down the Middle Boggy valley from near Shawnee Town, Rock Academy and the mouth of Little River to where one of the two trails marked crossed the Middle Boggy upstream of the Butterfield Line Road which runs generally east out of Boggy Depot. It should be noted that the OR Atlas Map actually matches the Plat of Boggy Depot per Muir. And I suspect that the road to Boggy Bottoms may be the trail used by Union forces. If this is the case then a site on the Middle Boggy closer to present day Phillips(imagine that!)or Lehigh both north of Atoka may be appropriate.
FWIW Feel free to correct me or shoot me down in flames.