I've got my map as follows:

DC Comics Presents 90 (not necessary but as explained above an interesting issue)
Captain Atom 1-6
Fury of Firestorm 63
The Weird 1-4 (this isn't necessary but I don't really have any place to put it so I put it here)
Captain Atom 7-10
Millennium 4
Captain Atom 11
Firestorm 68
Captain Atom 12
Captain Atom Annual 1
Captain Atom 13-22
Action Comics Weekly 627-631 (appears in the Green Lantern story)
Captain Atom Annual 2
Secret Origins 34 (can really go anywhere)
Captain Atom 23-57
Armageddon 2001 2
Armageddon: Alien Agenda 1-4 (the Armageddon issues finish his story, his next appearance isn't for another 1 1/2 years after this)