You just answered your own question there. Abraham Lincoln had no constitutional authority to free slaves in the north. As has been explained to you before the official stance of the United Stares government is that the confederacy was nothing more than a rebellion. Therefore the president, under his constitutional powers to supress rebellion, issued the Emancipation Proclamation. Now this was done after the US congress issued a series of warnings to the people in rebellion, through the second confiscation act, that they had sixty days to surrender or face confiscation of their land and properties.
So the emancipation proclamation was constitutional.
An act of congress cannot override a very specific constitutional clause. You must amend it. Article IV, *REQUIRES* slaves to be turned back to their masters if held by state law. It does not allow congress to override it by "confiscation acts".