Currently blocks are fully supported in backup & restore. The whole block structure will be saved in you backup files (position and visibility of each block) and restored at your destination.
In order to maintain backwards compatibility, in the restore process, if no block data is present, it automatically will create the default (current in Moodle) structure of blocks (the same that is used when a new course is created).
To use this feature (now in CVS), your backup and blocks version should be updated to 2004042100.
Please, test it with old and new backups. Any feedback will be welcome...
TIA and ciao, Eloy