monkeyscript is MonkeyScript's host environment binary. When run it basically sets up the environment then passes everything onto the central monkeyscript.js file which takes care of rc scripts, running a script file, and everything else.
There are a few special arguments to monkeyscript.js that will go to it instead of the script file. You can handle the separation by putting these before a script.js arg, and arguments meant for the script after that script.js argument.
monkeyscript -i [...]
This starts monkeyscript in interactive mode. If you include a script argument it will be run first then the REPL will be jumped into.
monkeyscript -h <name>
This is a monkeyscript script hook. Script hooks are special global scripts registered by a name inside of a rc script. For example, the system itself registers a "fastcgi" hook so web apps can be served out using FastCGI by running monkeyscript -h fastcgi inside of the directory of the web app.
monkeyscript --no-rc [...]
Using --no-rc empties out the default list of rc scripts to run. Generally this should be avoided unless you have a good reason to do it.
monkeyscript --rc <script> [...]
Using --rc adds another <script> into the list of rc scripts to run when invoked, you can use as many of these as you want and combine it with --no-rc if you really need to change the list or rc scripts that are run.