Hunter,
I go from Avid to Encore as well. When you go to export, click on options when it asks you to select a file. First, select audio and click that you would like to export the file as a WAV file. Click save, and chose a file name. Click okay. This will export the audio. Next export the video. Again, go to options. This time click on video, and chose to export the file as a quicktime movie (not quicktime reference). Hit save, name the file and export it.
When importing into Encore, go to Import as asset under the File icon. Import the audio first. You can transcode the audio now or at the end of the project either way the audio does not take long. Then import the video as an asset. The video because it is quicktime has to be transcoded immediately. I recommend a two pass when transcoding. This will take a while, but once done, you do not have to worry about it again. Then just create your timelines and the audio and video tracks will sync perfectly.
Steve