Of course they were, but there were plenty of Southern victories to point to, and I doubt if most southerners believed they were losing the war until after Gettysburg and Vicksburg, in 1863 -- if even then.
And the larger point I've tried to make here is that conflict actually began, not as a "war of Northern Aggression" but rather a "war of Southern Aggression" against the Union -- which included many seizures of Federal property and Southern invasions of Union states and territories.
If I remember right, one of the last of these invasions was the Early / McCausland burning of Chambersburg, Pennsylvania in July 1864.
Point is, the South launched many operations against the Union, and these did not end until the war was nearly over.
The Union took years to get geared-up, ramped-up, trained, equipped and effectively led to victory.
In the mean time, the South enjoyed some periods of relative success.
A misunderstanding on my part then. When you said that for two years the South had the best of the war I thought you were saying that they were winning.