After installation, all one simply has to do is type into Terminal:
$ mkvdts2ac3 path/to/file.mkv
If you don't want to keep the DTS track after conversion, add the -n flag to the above command:
mkvdts2ac3 -n path/to/file.mkv
[robg adds: Note that this hint requires an Apple TV that has been modified to run XMBC; here's one set of instructions for doing just that. I haven't tested this hint, as my Apple TV (though XMBC-enabled) is presently playing dead. :( ].

