well don't empty or drop tables unless you want the data gone
The empty function means you still have the table, but the info is gone, thus you can repopulate it with some info and drop means you'll delete the entire table.
I usually do the backup from the admin panel in phpBB. Still from time to time I go to phpmyadmin and select export. Then I select all tables and let it do the job. I am learning this stuff too so perhaps we'll have some other people contribute ideas in here
