I developed an application on Java that needs the following to run and be able to invoke a webservice throught HTTPS.
-Djavax.net.ssl.keyStore="C:\directory\local.keystore"
-Djavax.net.ssl.keyStorePassword=password
-Djavax.net.ssl.trustStore="C:\directory\local.keystore"
-Djavax.net.ssl.trustStorePassword=password
-javaagent:C:\directory\fakehostverification.jar
Now I am developing a similar application for Android with Eclipse Indigo, but I can't find the way to use those arguments.
Where I can set those arguments on Eclipse Indigo for an Android Project?
Is this possible? If not, what can I do?

Right click the project. Select Run as --> Run Configurations.
You can change the parameters passed to the JVM in the Arguments tab in the VM Arguments box.