The Emancipation Proclamation was an Executive Order related to the President's capacity as commander in chief of the army and navy. Any area which was taken under military authority of the united states, after January 1, 1863 (that is captured areas) any persons living in servitude there would be then, thenceforward and forever free
(I know I keep quoting Lincoln, but if a guy turns a nice phrase, it deserves quoting)
Habeus Corpus is a different matter, he did try and use the special circumstances granted in times of rebellion or insurrection (Article 1, Section 9, paragraph 2).