My method to restore a BackupBuddy backup was to first create a new Wordpress site
ee site create example.com —wp
Then to delete all the files that EasyEngine just created
rm -fr /var/www/example.com/htdocs/*
Then upload the backupbuddy archive and importbuddy.php
Navigate to example.com/importbuddy.php and proceed to restore as usual replacing all db tables when you reach the database restore step. Migrate the urls as usual.
The only thing to note is that EasyEngine puts the wp-config.php file up one level from the htdocs folder (wp will find it there and its probably safer), so when you’re done as the last step you will probably need to replace this wp-config.php file with the one that backupbuddy restored in your document root.