You don't even have to change it back to Manual. From my experience so far, the line-ups will "stick" with how you set them up even when set to Auto. Injuries are generally what causes things to get changed...if a starter gets injured, when he comes off the DL the cpu changes things all around.
What I've done is handle all the injury issues myself...it can be a little annoying/tedious, but it keeps me from having to mess with the line-ups too often. I use auto-fix for the minor league teams, but the pro teams I handle manually. Seems to have kept the line-ups I set almost perfectly so far.