From The Hospitals in Charlotte... by Michael Hardy (2010)
[We are going to] examine the city of Charlotte, and Mecklenburg County, during the War, by looking at the Confederate hospital in the city. Confederate hospitals were established in many of the major cities of the state, and along smaller towns that had rail access.
According to Kratt's Charlotte, Spirit of the South, in 1862, Charlotte's location on three rail lines resulted in Wayside Hospital, for the care of the sick and wounded soldiers going home and returning to the army. By 1863, extensive hospital buildings for several hundred patients were built by the Confederate government on the fairgrounds, a mile from town. By 1865, wounded soldiers in Raleigh and other cities threatened by Sherman were moved to Charlotte... The large school building vacated by the North Carolina Military Institute was used by Confederate officials as a medical laboratory. Late in the war, it also became a hospital, with Miss Maggie Graham as head nurse." (64)
It appears that there were many different facilities within Charlotte that were used as hospitals at different times throughout the war. In 1896, Miss Lily W. Long wrote an article for the Charlotte Observer, leaving us with these descriptions:
The first Hospital in Charlotte was established by the ladies in a large building used as the washhouse for the military institute, now the graded school. This building has since been removed. Here all arrangements were made for the care of passing soldiers. Every day two members of the hospital association went there with supplies of all necessary articles and gave their time and strengths to nursing and caring for our men. After a while the Confederate government took charge of the Wayside hospital, placed it under the care of the Medical department and used buildings of the Carolina Fair Association on what is now Middle Street, between Morehead and the railroad crossing, south....
The Charlotte women had little to do with the hospital work till near the close of the war when the tide of the battle surged into North Carolina. Many sick from Beauregard's and Johnston's commands and many from Averasboro were brought to Charlotte. The line of stores now occupied by E. M. Andrews and a old storehouse on the opposite side of Trade street called the Old Red House were hastily prepared for hospitals and again the women bravely took up the duty that came to hand and did everything that could be done for these poor fellows.
Based upon this information, there was a hospital in the washhouse on the grounds of the North Carolina Military Institute (was this the Wayside Hospital?); one located in the buildings on the fairgrounds; and then, at the close of the war, two hospitals located on Trade Street. The Wayside Hospital was Wayside Hospital No. 6, and the main Confederate Hospital was General Hospital No. 11. At the end of the war, according to Daniel Tompkin's History of Mecklenburg County, Dr. J. W. Ashby and Chaplain F. M. Kennedy (of the 28th NCT?) were in charge of the hospital facility.
This is not a lot of information on the hospital facilities in Charlotte. Maybe time and diligence in searching will produce more intel.