Note: When I use pointy brackets around a word or phrase, it means you should change the entire word or phrase, including the pointy brackets, to the thing I'm describing. For example, since my loginname is nancyg, I would use /Users/nancyg and /Users/nancyg/Desktop in place of the above.
Wherever you put the file, figure out the absolute path to the directory.
Here's a trick you can use on a Mac: use the finder to find a file (or directory, which is a special kind of file). Select the file, and copy it. Now open a terminal window and paste. The result is the absolute pathname for the file. You can use it in a command (eg, type ls followed by a space and then paste) or you can paste it into a text document or almost anywhere else that you need it.
Inside the BioNetGen directory are a number of subdirectories -- the most interesting are Models2, which contains a collection of models including toy-jim.bngl; Perl2, which contains a number of programs, most importantly BNG2.pl; and bin, which contains some more important programs and which will need to contain run_network (see instructions below).