I exported as a Quicktime and it exported as one file. Maybe I don't know enough about formats, but would a MPEG2 file automactically export as seperate files and if so, mabey my question is really for the Encore Forum to learn how to inport seperate files into a project.
Import the video file to Encore as a timeline, then the audio as an asset. Drag the audio file onto the audio track of the timeline.
Two separate files is the norm for authoring software like Encore, and it will take them them that way. If you're having trouble getting that working, a post over in the Encore forum may help resolve it.
Another way is export as MPEG2 - DVD and then choose DVD in the Multiplexer Tab
This will give you a single stream mpeg2 ( Audio / video combined in a single stream)
This you can use in Encore with out any need for Encore to do a transcode as well.
This ARTICLE might give you a bit more background on Multiplexing.
I always use Alan's workflow. In my case, I am doing DD 5.1 SS, so I need to Encode it separately anyway. Also, make sure that your Audio specs. are exactly what Encore wants. It is neither a video, nor audio editor, and is very sensitive to what it will accept and work with properly. Give it what it wants, and it will work well for you.
FYI - you can actually use the Import as Timeline dialogue to import the audio AND video assets simultaneously (so that you don't have to import the video as a timeline, then select the audio for import, then drag to the timeline).
In the import dialogue, just selec the audio and video assets that go together on the timeline and import them. The timeline will be complete in 1 step instead of 3.
And no transcoding required if you use a Dolby encoding option from the PPro export dialogue.