Two documents you need look at:
1. The Articles of War (first passed by the Continental Congress in June of 1775; major amendment in September of 1776). These lay out the rules and punishments, how court martials were organized etc. There were some amendments in April of 1777, but after that they remained pretty much unchanged until 1805. They are available online at http://memory.loc.gov/ammem/amlaw/lwjclink.html#ci
Select volume 5, and then "Navigator" and scroll down to 20 September 1776.
2. Regulation for the Order of Discipline of the Troops of the United States (1779) the so called "Blue Book". This manual has the manual of arms for the troops. If you were ever in the army, it is the equivalent of FM 22-5. Baron von Steuben wrote the manual and it was approved by the Continental Congress on 29 March 1779. It was reprinted many times (but I don't know if it was updated or not). The last edition my source (Baron Von Steuben and his Regulations-- Joseph R. Riling, Ray Riling Arms Books Co. 1966) lists is 1809. It contains the manual of arms, rules for setting up a camp, guards, sick, and a section of instructions for different positions: Regimental Commander, Adjutant, Quartermaster, etc. This part of the regulations has been digitized and is online at http://www.quartermaster.lee.army.mil/qm-bluebook.Html
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