You might find the following thread relevant: Arky ;o)

I think SoftEncode is the best program out there for AC3 encoding, but make sure you set the smapling rate to the kz (I'll get the right one when I find it) CoolEdit is an awesome program for editing audio, changing sampling rate, adding effects, and converting IMO. It's really easy to use and works the best for this type of thing. I made the music for my first-play DVD logo's using this. CoolEdit and Soft Encode are great ! Though Soft Encode makes the volume kinda low.... but I probably can fix that I just haven't tried.

help with soft encode 

can somebody tell me how to encode a ac3 2 channel audio file from a 5.1 ac3 file in soft encode? Or any other program for that matter

Well it should by itself encode it to 5.1 unless there is settings I didn't know about, so once you start it up, open a new project and load your audio file. If it doesn't load, convert it to WAV and then it will load. SoftEncode is incredibly simple and easy to work, so it should be too much trouble.

Tried Besweet & Softencode 

Perhaps decode it to 2-channel wav in Besweet and encode it to ac3 in SFSE is the best way to do it then?