Ninite works great along with other automation tools or scripts you may be using. The main switch you'll want to keep in mind is our /silent mode. Often you'll may want to use "/silent ." as the option to output any reporting to stdout.
Ninite Pro's command-line selection will probably be quite useful too.
You may want to use the /cachepath switch to cache files on a local share to save bandwidth.
Besides that, just keep the Ninite command-line reference handy and everything should be fairly straightforward.
These features are only available in Ninite Pro Classic.
We're working on documentation for the new Pro web interface. For now the available help for that is inline in the interface.