Sorry that I still didn't make myself clear. In Rifles for Watie, guerrilla-TYPE raids are made on Union supply lines which left me with an initial impression that Watie's forces were guerrillas. But as I corrected myself, as pointed out by Bama, Watie and his forces were commissioned as regulars in the CSA.
The difference between guerrillas and regular forces is that guerrillas operate behind enemy lines; out of uniform with no insignia; and not under the command of the leadership of a regularized armed force (that is, in uniforms, with insignia). It is this "out of uniform" identity that makes them guilty of war crimes by definition, whether they fight the enemy or civilians. The same with spies--which is why they are prime targets for hanging trees. This is also why thousands of military commission trials, similar to those being held in Guantanamo now, were held, not to determine if someone was out of uniform, but to determine if they actually engaged in hostilities which would make them guilty of war crimes. In other words, if you're out of uniform, your enemy has to have evidence that you were fighting him to deem you a belligerent. If you're in uniform, you're a belligerent by definition, and coverd by the laws of war. However, technically speaking the whole Confederate Army was not part of a "regular" force as the US govt. never recognized the soveriegnty of the Confederate nation. However, given that the CS had mobililzed an armed belligerent force of sufficient strength to engage the regular US Army in combat as equals, the US govt. accorded the CS forces "de facto" belligerent status, giving soldiers POW status, and thus the protections of the international laws of war that existed at the time.
All of these war powers questions are very much relevant in the current terrorism and Guantanamo debates--exact same issues and very few Supreme Ct. cases on it. Anna Ella Carroll published her political/legal pamphlets discussing these issues that helped keep Maryland loyal--showing that Lincoln's use of his war powers did accord with the Constitution and internationa laws. I reprint her 4 major pamphlets in my book. E.g., the reason that the Emanc. Procl. only covered the CS was that, given that it was issued under Lincoln's powers as commander-in-chief, as a military measure (since slaves contributed to the organized forces of the rebellion), the proclamation could only be issued in territory which was governed by martial law, which the belligerent area of the CS was, or would be once the US forces fully invaded and occupied.