I haven't played Fallout 3, but if you're playing on a console I could help.
Depending on how far both of you are, you could just make a new profile on the console (PS3 or 360) and one person can play on the current profile, and the other can play on the new profile so you each have your own set of game saves.
The only downside is that if you have a 360 with Live, you could only play Live on that account.