Basically, Bottom Logan choice happens pretty early, if you encourage him to confront the bandits. Discouraging him gives you normal/Top Logan. You'll probably know if you have Bottom Logan, as he'll have a number of scenes you can stumble across of him power-bottoming other characters.
As far as the hearts go, the main one that's missable is during the werewolf event. When you have to make a choice to go after either Bernard or Logan, you have to choose Logan. Logan's the better choice there if you're trying to get hearts on everyone, as Bernard's hearts don't depend on this choice.