How does one vote for "lesser evil" when both are, in one's opinion, firmly entrenched in the 7th level of hell?
Easy. Because even if they're equally evil, they aren't equal in their effect on the government.
If it looks likely that they're equally evil, and the polls indicate that the Congress and Senate are going to go to one party, then if you believe in divided government and checks-and-balances it can be argued that you have an obligation to vote for the candidate in the opposite party of the one that will have the Congress.
Of course, since candidates are never equally evil, it's an academic choice. Also, if you believe divided government is not an effective litmus test, then you can apply a similar test of your choice. In the end, it's never an equal choice.
You're right that the electoral college has the biggest impact at the moment. If you really feel strongly about the evilisciousness of the candidates, you should make your choice known in the primary on 2/5/2008 (and support your candidate before then).
Cheers,
Scott.