munger is a wrapper script which coordinates running registration and warp for many brains. There are some sample parameters which have been widely used for fly brains. I believe similar paramo have also been used for larval fish brains by e.g. Mike Orger, Owen Randlett, Michael Kunst, Ruben Portugues.

You might like to try the Fiji CMTK GUI (ask google) to generate scripts that call munger. The -awr flags you mentioned are arguments to munger not to CMTK.