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A 64bit compatible program just means it'll work on a 64bit OS. To really see faster encoding speeds the program needs to be able to take advantage of multiple threads. And then it's a matter of how many threads it can work with.
Unfortunately Premiere Pro and the Adobe Media Encoder are still 32 bit (the only 64bit proggy is 64bit Photoshop).
I find there to be a huge difference in encoding on a Core i7 machine vs. say the Core 2 Duo or Quads though. So unless you're going the GPU encoding route, the processor does matter a great deal.
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