If one a single agent has conflicting desires (each of which it values equally) then it should work to alter its desires, so it chooses consistent desires that are most likely to be fulfilled.

To your latter question though, I think that what you're asking is "If two agents have utility functions that clash, which one is to be preferred?" Is it that all we can say is "Whichever one has the most resources and most optimisation power/intelligence will be able to put its goals into action and prevent the other one from fully acting upon its"?

Well, I think that the point Eliezer has talked about a few times before is that there is no ultimate morality, written into the universe that will affect any agent so as to act it out. You can't reason with an agent which has a totally different utility function. The only reason that we can argue with humans is that they're only human, and thus we share many desires. Figuring out morality isn't going to give you the powers to talk down Clippy from killing you for more paper clips. You aren't going to show how human 'morality', which actualises what humans prefer, is any more preferable than 'Clippy' ethics. He is just going to kill you.

So, let's now figure out exactly what we want most, (if we had our own CEV) and then go out and do it. Nobody else is gonna do it for us.

EDIT: First sentence 'conflicting desires'; I meant to say 'in principle unresolvable' like 'x' and '~x'. Of course, for most situations, you have multiple desires that clash, and you just have to perform utility calculations to figure out what to do.