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We actually blogged about this a week or two ago as the documentation doesn't really go into this and combining ATG Personalization with Endeca Experience Manager is extremely powerful... http://wp.me/p2XJtl-3z
To save you a click, you can use the runcommand script for your application to accomplish this in an "adhoc" fashion:
./runcommand.sh IFCR importNode ../config/ifcr/userSegments userSegments
This will update the user segments available in Experience Manager without having to re-run initialize services. You can also script it in your AppConfig scripts so that it can run as part of the update cycle.
Thanks Patrick. This really helped.