OK, assume I know nothing and you won't be far off

In this situation, I assume that I need a tool to split the container file (mkv, avi, mp4...) into the separate audio and video streams, then I need another tool to convert 6 channel AAC to AC3 5.1, then I need another tool (or maybe back to the first one) to put it all back together.
Whew...
This sounds A) too complicated, and B) slow.
Is there a way to do this in one step, and hopefully not recode the video to save time?
If not, what do the users here recommend for the above three tools?