The -c option says which configuration you plan on using, (default, minimal, all etc). When using run.bat directly you should probably add elements to the classpath.
If you run run.bat -h you should probably see common flags to set.
There it says you need -C (capital letter, not lowercase) or --classpath= to add elements to the classpath.
So the only difference between run.bat and eclpse is that elcipse gives you a nice graphical way to edit the classpath, whereas via command line that responsibility is yours.