You can create multiple profiles to keep saves from different playthroughs separate.
The number of quick and auto saves kept can be increased in the gameplay section of the options.
Co-op is drop-in/drop-out, so a game can be started as single player or multiplayer, and switched back and forth.
Theoretically it would be possible to add a unique code during character creation, though, and check that when overwriting saves, to pop up a warning if there was a difference.