it's strange, we are at 2014, you think that a proper save system would be in place by then, but then again, this is Obsidian Entertainment we are talking about, i guess since this game isnt that glitchy, they had to compensate with something else.
Uh you can still have multiple saves, it will just save to that checkpoint. Manual saves are not automatically overwritten.
The fact that it is tied to checkpoint would normally bother me, but there are so many checkpoints, almost every area change gives you one.
Except for when you grab something, go to fight a boss in an area you leave and can't come back to, LOSE and then forget to grab the something again before you go back in and whup it's behind. Which is what happened to me and screwed me out of not one but TWO achievements on the first time through.