So just make sure no one sees me when I'm taking the guards down? I never understand what it means by alert; is that not letting them see the bodies or just not being seen?
If you haven't done it yet, the important thing is to not alert anyone. Once you do, the guards respawn forever.
How the hell do I beat Two Face at the end?
I took out everyone except Two Face and the guard on the bridge. Chucked some Caltrops at the other one and pounced on Two Face, then beat the fuck out of him, pausing to beat the other guy when he got up. Knock Two Face down a few more times, and done. The section ends as soon as you beat him.