The standard Emacs indentation behavior is to indent on TAB rather than newline. This is also the default for Lisp-mode, as far as I know. You can rebind this by setting RET to comment-indent-new-line, though.
You need to add some argument to mzscheme to get it to cd into the arc directory. Check the args passed in arc.sh.
Ok, thanks. I hacked a batch file and put it in my PATH so I can start arc from emacs. (Setting arc-program-name failed because run-arc wouldn't respect the quotes around the executable name.)