You can just add those tomee config files to your eclipse server config folder and continue using the "use workspace metadata" option. I find it much better to configure tomee servers for eclipse that way. For example, if you just copy tomee.xml and system.properties from your tomee installation conf folder using explorer and then select your server configuration in the eclipse project explorer (eg. Servers > apache-tomee-plus-1.5.2 in my case), then paste those files there. If you then do a republish, those files will appear in the .metadata/.plugins/org.eclipse.wst.server.core/tmp/conf folder and you should have a properly configured server. No need to "use tomcat installation". In fact i avoid that because you may need slightly different tomee configurations for different projects.
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