Not an avid researcher, I'm snooping around looking for whatever I can find about my great-great-grandfather, John Frank Johnson. From http://www.rootsweb.com/~vascott/48th/sparjfj.htm (before it became a dead link) I found:

John Frank Johnson
Rank: Private
1860 Census: Company I, 48th Virginia Regiment
Enlistment: Washington Co., age 29, 6/18/61.
Present thru 10/15/61.
Hospital, sick by 10/31/61.
Hospital rheumatism, Charlottesville, 1/2/62 to 3/10/62 when released to duty.
Captured Cross Keys 6/8/62.
Paroled Winchester, age 29, 6/62.
POW aboard Steamer Coatzacoalcos following capture at Cross Keys. 5'4" in 1862.

He's of interest for me because he apparently fought for the Confederate army, then was moving to Illinois after the war when he headed back to VA, left his family, and relocated to McDowell Co. in WV. Family myth and lore call him a turncoat and a traitor, but there's no evidence I can find for that.

Where should I look online? Where should I go to find archival records?