[Mylenium] “You need to encode your audio file accordingly using the options provided e.g. in Audition.”
Audition will handle creating a 5.1 mix and exporting this mix in a couple of different ways. Unfortunately Encore will not be able to use any of these exports directly. The first issue is that Encore only encodes stereo ac3 (dolby) files. Secondly, it will not open a multichannel file that you could create with Audition.
You need other software (or hardware) to encode a surround sound dolby file.
Adobe Premiere Pro (with an optional plug-in) can create and export surround sound encodes that can be used by Encore. You could also probably accomplish the 5.1 mix with Premiere Pro but might find Audition to be better suited to the task. The Audition exports would be used by PPro to encode the dolby file to be used by Encore.
Creating surround sound mixes is probably a career unto itself. Expect to spend a lot of time climbing the learning curve before you get useable product – or hire an expert.
Dave