Same situation here, it would have been nice if DOE made it clearer to us how many alternates there were, etc. But we can't really complain! I am planning to just call NSF if I decide to take the DOE. The NSF decision deadline is May 1st so I think if you talk to them before then it shouldn't be a problem.
Did anyone else get selected as an "alternate" for the DOE, or have any idea how many alternates there are? I can't imagine people turning down the fellowship so I am not sure what good it does me above being a finalist.