Anyone saying "use multiple saves" probably hasn't heard of the PS3 bug and I'm guessing the OP is playing on the PS3. My brother who plays in the PS3 had a few manual saves but when he made a new character they all got deleted and he had to start over again.
Not sure if there is some sort of a limit where if you perhaps have over 10 manual saves you're in the clear but two or three doesn't seem to cut it when it comes to this bug.
I play on PS3, got 3 save files. (+ three auto-saves). No problem at all when starting a new character, the old files are still there. I do, however, manually save over them anyways because I don't want them there. An USB-stick will make it 100% safe to start a new character though.
(no idea what is making some other ps3's delete the old saves automatically, even when there's more than 1 of them there)