Seems to me if there are airplanes it favors the Union.
Not just because of the larger industrial base but for the simple perspective is that even the earliest incarnations of World War era airplanes eliminate what was one of the major southern advantages.
Lee's mobility. There is no suprise. McClellan isnt going to be to be having nightmares that Lee outnumbers him.
Lee is going to have a much more difficult time stealing a march on the Union with Union Spotter planes on the lookout for his army of Northern Virginia. When he splits his army for manuvers it will be seen. Sure its not real time but a plane flying over observing(No photographs) and returning is still a lot quicker then moving an entire civil war brigade or wing into position.
The most significant thing though is wether or not the machine gun is invented early as well.
If it is and the South can make some that would have a bigger effect on the outcome of the war as it works better in a defensive setting thus negating some of the effects of larger northern production of it *but not by much* IMHO.
But if we assume it does and our focus is the Air. I figure northern and Southern pilots are going to be a bout equal. Unlike the advantage the south has in a large segment of trained marksmen and horse riders the airplane is going to be new. It will come down to time in the saddle and number's. The Union will put more in the air then the South. Barring them getting lucky and figuring out just what to do with them by sheer luck before the Union does they get slaughtered in the skies as the Union can simply afford more planes, more pilots, more flight time and to send more fighting scouts at one time against the Confederates.
Which is still useful for the Confederates as a delaying measure if the planes are to busy tangling in the sky and the brigades,wings,armies get into position to pound the damnyankees.
Course if they don't the Spotter planes would still be the mainevent. Were not talking about precision bombing taking out artillery batteries. The scouting role will be the airplanes importance in the civil war. Far outweighing the odd artillery peice put out of action by a strafing run, or general nusiance of advancing infantry.
Feel free to point out the holes in my logic.