Using migration tool for several jboss 6.4 instances

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I have jboss EAP 6.4 in /some_directory/jboss-eap-6.4
My instances are in /some_other_directory/instance_name.

If I specify the instance directory the tool stops and complains about jboss version.
If I specify the jboss 6.4 directory the migration tool migrates the standalone.xml which we don't use at all.
How can I use the migration tool?
Should I copy the instance's standalone-full-ha.xml to the jboss directory first?
Should I copy other directories and file too?

Jeroen P.