There wasn't much to the remains of Ft Towson during the war. Doaksville, on the other hand, was a prosperous community and economic center of the Choctaw Nation. It seems they were at times used interchangeably as if they were the same place. In one of Maxey's reports, he addresses it from his headquarters at Ft Towson and then says he is at Doaksville in the report. Doaksville was only a few buildings but there was probably a sizeable community within a five mile radius and the whole area would be referred to as Doaksville (people usually didn't live within less than a quarter mile of each other.)
Below are some sources re Ft Towson/Doaksville...
The first is an extract from the Chronicles of Oklahoma (Vol.8, No.2, June 1930, Page 226) regarding Ft Towson and Doaksville during the war:
After the soldiers left, the buildings were placed in charge of the Indian Agent, Douglas H. Cooper, to be used for purposes of Indian administration. A few years later a fire broke out that destroyed all of the buildings except the hospital and one of the barracks. These remaining buildings were occupied by the Confederates during the Civil War, and General S. B. Maxey made it his headquarters in 1864. Thus the old Fort was quite a busy place and retained its importance until the close of the War. After that time the few buildings that survived soon fell into ruins, most of the materials—even the foundation stones—being hauled off by the people in the surrounding country.
We should speak briefly of Doaksville, as the little town was called that sprang up about a mile west of the Fort, taking its name from the trading station two brothers named Doak first established on Red River at the mouth of Kiamichi. Doaksville became the trading center, the site of the Indian Agency, and from 1850 to 1860, the capital of the Choctaw Nation. Here in 1837 the Choctaws and Chickasaws entered into a joint treaty with the United States and one another, by which the Chickasaw acquired homes within the Choctaw territory and promptly removed to Oklahoma. Here was held the famous Choctaw convention of 1860 which drafted the Doaksville Constitution under which the Nation operated thereafter. The first Masonic lodge in Oklahoma was instituted at Doaksville, to which many of the army officers and missionaries belonged. In the old Doaksville cemetery, now a part of the cemetery of the town of Fort Towson, lie the bodies of Colonel David Folsom and Colonel J. H. Nail, both of whom led parties of Choctaws from Mississippi to Oklahoma, and became founders of families still prominent in the eastern section of the state.
The full article is at:
http://digital.library.okstate.edu/Chronicles/v008/v008p226.html
Chronicles of Oklahoma
Volume 17, No. 4
December, 1939
DIARY OF A MISSIONARY TO THE CHOCTAWS
1860-1861
Edited by Anna Lewis
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Fort Towson, Ind. Ter., and such other points as may be selected by
Brig.-Gen. Cooper, commanding District of Indian Territory, are
designated as places where the paroles will be administered and the
public property turned over in accordance with the terms of surrender
agreed upon by Maj.-Gen. Canby, U. S. Army, commanding Army
and Division of West Mississippi, and Gen. E. Kirby Smith, C. S.
Army, commanding Trans-Mississippi Department, at Galveston, Tex.,
June 2, 1865.
E. KIRBY SMITH,
Gen.
ORs Series I. Vol. 48. Part II, PAGE 728