Helen --

I'll try to answer some of your questions.

I've spent several years researching Alabama militia in the late antebellum period (1859-1860) and presented a paper to the Alabama Historical Society on this organization. In essence the militia existed just like juries exist today. The state has the right to call you into service for jury duty, and you must respond unless excused by lawful authority. After John Brown's attack on Harper's Ferry, the state legislature recognized that militia in its current form was completely inadequate. To fill the void, an act passed in February 1860 creating the Alabama Volunteer Corps. By May 1861 almost two hundred companies had been organized, uniformed, trained and equipped under the AVC act. Nearly all had been armed with modern weapons by Governor Moore.

Boykin's company, the "Mathews Rangers", was NOT an AVC or militia company, being organized after the AVC was abolished by the legislature (November 1861).

Boykin's company was assigned to duty along the Gulf Coast (Mobile and Pensacola). To review official documents from South Alabama and West Florida for the period 1861-62, start here:
http://ebooks.library.cornell.edu/m/moawar/waro.html
Volume VI. 1882. (Vol. 6, Chap. 15-16)

You can spend years reading about Colin McRae. For starters, here you go:

http://www.amazon.com/Colin-McRae-Confederate-Financial-Agent/dp/0979587417
http://www.crr.sc.gov/Research1/McRae%20Business%20Papers%20Finding%20Aid_10-4-10.pdf
http://www.lib.ua.edu/content/findingaids/pdf/mss_1261.pdf
http://www.encyclopediaofalabama.org/face/Article.jsp?id=h-2331

Also, read this discussion about destruction of papers and where relevant sources have been uncovered:
http://civilwartalk.com/threads/william-b-edwards-classic-book-civil-war-guns.97685/

As previously mentioned, Boykin left his company in February 1862. Since Adley H Gladden was mortally wounded at Shiloh on Apr 6, 1862, any presumed association with Boykin as a civilian could have lasted only a few days. I've reviewed General Gladden's papers nd find nothing about civilian aides as staff members.

Robert E Lee was assigned to command on June 1, 1862, after General Joseph E Johnston was disabled by wounds. Lee organized that army as he thought best but was always limited by what President Davis (and Congress) would allow or concede. Lee sometimes made suggestions about other Confederate forces. However, he had no responsibility or direct command over other armies until very, very late in the war.

Congress passed an Act on Feb 17, 1864, which established Junior and Senior Reserves. Boykin was conscripted under this act, being an able-bodied white man between the ages of 45 and 50.

Hopefully this is a start . . .