THEMES are totally rewritten in Moodle 2.x I do not think they can simply be imported through backup-zip-files.
Besides that migration from 1.9x line to 2.x line is to create a clone/exact copy of your production site, then upgrade this clone to the latest Moodle 2.x you want, do automated backups of every course and finally install a new fresh Moodle 2.x on a separate server, transfer the course-backup-files there and restore them there. This way you never lose your production server and you can repeat the procedure as many times as needed without ever touching your production server. Even after switching to the new server you can continue to run your old server until shutting it down.
Rosario