The answer to your question is much too long to go into indepth, but the short answer is that if he was stationed at a hospital, he would not show up in regimental records (unless he was previously or subsequently a regimental Surgeon). He also would not show up in State records (again, unless he has previously or subsequently been assigned to a regiment).

He would/should show up in the National Archives microfilm of records of Confederate Medical personel. You should start with these:

M119-109.8 RECORDS OF THE MEDICAL DEPARTMENT, CONFEDERATE WAR DEPARTMENT, 1861-65

M119-109.8.1 Records of the Surgeon General's Office

M119-109.8.2 Records of Medical Directors

109.8.4 Records of hospitals

See http://www.archives.gov/publications/prologue/spring_1994_confederate_medical_personnel.html for further research tips.