There were two main disadvantages for the North at the beginning of the Civil War. I will describe both of them here.
First, the North had much less of a military tradition and therefore much less military leadership. The US Army before secession had not been terribly big. Moreover, most of its best officers came from the South. The South had more of a tradition of military service. Men in the South were much more likely than men in the North to know how to ride and shoot well. The North was at a major disadvantage in this way.
More importantly, however, the North had a much harder strategic job to do in this war. The North had to invade and subjugate the entire South. In order to win, the North had to actually conquer the South. By contrast, in order for the South to win, all it had to do was hold on until the North got tired of fighting and came to some agreement with the South. This was, at the beginning of the war, probably the most important disadvantage faced by the North.