What do you mean by initial bat command.
You can rerip->encode just the soundtrack if you want.
I just ripped "I am legend" and I picked the specific tracks I wanted.
Here is an example of my .bat file.
d:\\hd\\eac3to\\eac3to.exe "E:\\BDMV\\STREAM\\00000.m2ts" 1: "d:\\HD\\iamlegend\\iamlegend_chapters.txt" 2: "d:\\HD\\iamlegend\\iamlegend.mkv" 3: "d:\\HD\\iamlegend\\english.ac3" 4: "d:\\HD\\iamlegend\\englishtruehd.flac" 11: "d:\\HD\\iamlegend\\eng.sup" 27: "d:\\HD\\iamlegend\\swe.sup"
So the numbers and the colon selects which track to pull, e.g 1:, 27:
If you look at the 4:, that was the TrueHD track, if you just put the extension to whatever you want it to be eac3to will handle it, e.g. in my case englishtruehd.flac
You can also get more examples from the wiki if you want.http://en.wikibooks.org/wiki/Eac3to/How_to_Use