Then how do I get sound into the file that I converted. Also I have no clue what muxing is or how to do it. Can you explain?

Do look in this thread where I do think how to mux your encode with an encoded audiostream is explained.

http://www.kvcd.net/portal/articles.php?lng=en&pg=34

Hi guys,
Inc., that's BP's guide and he used Tok so I guess there's no explaining how to mux video+audio as it was done automatically by Tok.
Also Adam was testing Mencoder and that guide covers Tmpgenc.
This is not going to be an easy thing
Do you suppose you could add Packshot MP2 support?
That would really help newbies
And some oldtimers too
Cheers

__________________
Rui