The manpath tool is a little dumb. The manpage claims that it tries to find other manpage directories in by looking at your $path variable, but it never worked for me. The only way I was able to get the alternate manpage paths into it was by editing the manpath config file.

After reviewing the manpath manpage, I located the config file (/etc/manpath.config) and popped it open in BBEdit. Part of it looked like this:

#
# set up PATH to MANPATH mapping
#
MANPATH_MAP /bin            /usr/share/man
MANPATH_MAP /usr/bin        /usr/share/man
MANPATH_MAP /usr/local/bin      /usr/local/man
MANPATH_MAP /usr/X11R6/bin      /usr/X11R6/man

I added a couple lines to that part:

MANPATH_MAP /sw/bin         /sw/share/man
MANPATH_MAP /opt/local/bin  /opt/local/man

Basically, these lines say "If (x) is in the user's path, add (y) to the manpath." You can add as many of these as you need to get your manpages working. The two that I added were for the fink project and darwinports.