Terminal command to select newly deployed node-red project?

I've created a .deb package that deploys my node-red project into the correct directory structure. However when I start node-red it uses a default flows file. Is there a command that I can run after deployment that will set my newly deployed files as the current project? Or is it a line I can add to the settings file? Thanks!

You can either pass the flow fie name as a command line parameter when starting Node-RED or look at the setting file line 68

Is it just the flows file that is the wrong one or is it using the wrong settings file also? The flows file that it runs defaults to one containing the server name, so if the same flow is to run on multiple servers you can use the command as @dceejay suggests.

Thanks dceejay, adding that line to the settings file was exactly what I needed.