Generally you will find the soldiers enlisted in the counties where they lived, in this case I suggest looking at the William Miller in the 1850 & 1860 Wilkinson County Census as the probable member of Companies E & D, 21st. Miss. Infantry.

After the war, William F. Miller can also be found in the census records of Catahoula Parish, Louisiana which is where he filed for a Confederate Pension.

Louisiana Secretary of State
Confederate Pension Applications Index Database
Selected Name Detailed Data

Reel: CP1.98 -- Microdex 2 -- Sequence 25
Target card: MILLER, W. F.

Applicant Information & Name Variations:

MILLER, WILLIAM F.
Parish: CATAHOULA -- Pages: 13

Soldier Information & Variations:

MILLER, WILLIAM F.
State: MS
Unit: 21ST REGIMENT
Company: STAMP'S CO.

State: MS
Branch: INFANTRY
Unit: 21ST REGIMENT
Company: CO. E
(Above military data is from the War Department.)