I don’t really use ffmpeg much, so I can’t really comment on that, but eac3to can’t work with individual wav channels and output an aac file. You would have to merge the wav files to a six channel wav and a separate stereo wav somehow first.

You could try using the program AudioMuxer, it has some tools that might work.

If it were me, I would use some combination of wavewizard to merge the files and eac3to to do the conversion. It’s not automated but it doesn’t take that much effort. Watch out with wavewizard though, as it tends to write the riff headers incorrectly for multichannel wav files. I don’t think that will really matter when using eac3to, for what it’s worth.

Also, look for a GUI for eac3to called Useac3to, I find it makes re-encoding much less tedious than typing in the command lines for everything you want to do.