You'll get better with practice, but keep in mind distance plays a major role.
http://www.dofmaster.com/dofjs.html
If you're very close and your lens is super wide open, your depth of field really IS razor thin. Perfectly focused on eyes from four feet away is going to put the tip of most noses out of focus. If you're testing on a book from a minimal focus distance away, you're lucky to get multiple LETTERS in focus. Doing it manually versus automatically isn't going to change any of that. It's just the maths involved!