Were they basically propaganda machines for the Confederacy? Did they maintain objectivity? Were they critical of generals or the government?
Did they maintain objectivity
I can't answer all of your question, but in graduate school I did work on newspapers in a border state after the Civil War. It's very important to remember that the notion that newspapers should be "objective" (by which, really, we mean "neutral") did not exist during the Civil War nor did it exist in the years leading up to the Civil War.
(Objectivity as a construct arguably dates to around the turn of the 20th century, when the newspaper profession was becoming "professionalized" and "scientific," and it's definitely tied to the rise of advertising as the profit center for newspapers, and it also never really caught on in smaller places or even in a lot of big city newspapers, and it's something that a lot of places only still give lip service to. But I digress.)
Before the CW, newspapers were essentially party organs, and there's a good argument to be made that newspapers were a major organizing factor around the formation of political parties during the Jacksonian period. Newspapers of the period leading up to, during, and after the Civil War were rancorously partisan, often in competition with newspapers in the same town or in competition with newspapers in bordering towns, counties or states. Newspapers were not propaganda machines for "the Confederacy" any more than northern newspapers were propaganda for "the Union;" rather, they tended to be propaganda for their political party/affiliation. The time period I studied (roughly 1867-1880) had sharp divides between formerly Unionist and formerly Confederate papers, and bitter personal attacks in print were fairly common.