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By default the modules folder is stored in a folder named "modules" in the application data directory. If you change the app dir directory for each instance you don't need to change the modules folder. However, if you use the same app dir for each instance (not advised for production, ok for testing), you should change the folder where modules are stored using the global property setting (formerly Global Property from 1.8 downwards)module_repository_folder. You can use either a relative path (relative to the app dir) or an absolute path.
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The standard "mvn jetty:run" command in the webapp folder starts "openmrs" on port 8080. You can start a second instance of openmrs on a different port and with a different context path by using two Java properties: webapp.name and jetty.port:
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mvn jetty:run -Dwebapp.name=openmrs2 -Djetty.port=8081
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You might want to change the location of the application data directory using a runtime property. You can also change the folder where modules are stored using a global propertysetting (formerly Global Property from 1.8 downwards): module_repository_folder. You can use either a relative path or an absolute path.