Len --

First, I believe you mean Southern militia rather than Confederate militia. The words 'Confederate' and 'militia' are mutually exclusive, the same as 'national' and 'local'.

Militia units are always local in nature and primarily raised for self defense. In January 1861, before the Confederacy organized, volunteer state militia units from Alabama were invited to Pensacola by the Governor of Florida. I'm sure there were other situations like this in early 1861. They would be highly unusual afterwards.

To my best knowledge, no militia unit from any state (let alone any of the territories) was ever assigned to the Army of Northern Virginia. Confederate quartermasters were not authorized to issue pay, arms, equipment or uniforms to state militia officers. For this reason, militiamen would not last long in the Confederate army.