As I recall, it's really easy to use. There's an option to convert an indivual MKV file with 6ch aac to 6ch AC3, or convert the whole folder.
I test out with 1 file, make sure it work, then move all files I want to convert to a folder, and convert the whole folder. I used mediainfo to find out which
aac files I want to convert. If output folder=input folder, the file will be created as xxx_AC3.MKV. Each file probbaly take 10-15 minute to complete.
The setting have a tab to convert DTS to AC3, if checked, will convert DTS (5.1) to AC3 (5.1), another tab to convert AAC (2ch or 6ch) to AC3. Each section have a selection for the bitrate you to use. The video is untouch for sure as it use MKVExtract, MKVMerge etc... from MKVToolnix to do the demuxing & remuxing. Just the audio portion being convert.
For me the pain is come from converting an MP4 with 6ch aac file to MKV 6ch aac files. I would be using MKVToolnix GUI, add MP4 file, make sure compression header for both Video and Audio is 'none', and then convert (remuxing) to MKV file. I don't know why I took so long for the GUI to respond (more than 5 minutes wait) after I add an MP4 file in.
That's my experience. I hope that help.