As mentioned above, you should use desktop policies for this task. In addition there is also available managed setting tab, where you can put settings for the embedded Sametime plug-in. For example, I have used the following settings:
com.ibm.collaboration.realtime.community/host=SAMETIME_SERVER_HOST_NAME;
com.ibm.collaboration.realtime.community/name=SAMETIME_SERVER_HOST_NAME;
com.ibm.collaboration.realtime.community/port=1533;
com.ibm.collaboration.realtime.community/loginByToken=true;
com.ibm.collaboration.realtime.community/loginAtStartup=true;
com.ibm.collaboration.realtime.login/autologin=true;
com.ibm.collaboration.realtime.login/resetUser=true;