Thought maybe someone can help me out on this. Just wanted to know,in MovieStacker's Audio Stream tab, if I have to set BOTH kbps Audio 1 and Audio 2.....when my HeadAC3he options are set for: "Dual Channel" ???

No, I think that is just a bitrate calculator for an SVCD with two audio streams. If you're using HeadAC3he you shouldn't need to feed the audio into Avisynth.