Reading his letters to his family is a good clue. My humble understanding is that he never expected to win a war. The best that he felt he could hope for was to make the conflict so costly and abhorrent to the northern voters, that northern voters would demand the northern government to negotiate peace. He understood from the start that if the north kept it's will to fight that eventually the south would be crushed. I have always thought the same thing.
If you read first hand accounts, those books say that there were a lot of men, including Lee, who didn't want to fight anyone. One first hand account/book said that the biggest recruiter for the southern forces was the northern army. It said that when the northern forces invaded Virginia, the atrocities they committed forced men, especially along the border, into the army to defend their families. And that those atrocities were the biggest recruiter for Morgan.