The claas that you created in Eclipse will be committed to the teamserver SVN and will be used in the packages you build when you add the class in the same package for example. This class will then end up in the javasource directory under the module you’ve build the class in.
Placing the class somewhere completely different will result in the class not being picked up when building a package. If this is a requirement somehow, then export your class as a jar file and add the jar file to the userlib directory to make sure you are able to access the class from the “action’ class that is created from your Mendix java action.
For an example of additional classes have a look at the SAML module e.g. from the market place