The SAP MII product is based on top of the standard NetWeaver UME and will work with the standard SAP NetWeaver SSO configuration. Perhaps a guide like this one will be sufficient to guide you on setting of SSO with NetWeaver and your Java application: http://scn.sap.com/community/sso/blog/2012/08/17/how-to-configure-sap-netweaver-single-sign-on-with-certificates-out-of-the-box
Sam
