You don't need to backup ~/MyDocs.. you can do that using a PC.. turn phone off, plug in and you'll be able to access the mass storage..

the backup script backs up /home/user but NOT /home/user/MyDocs.. which is where all the settings and config are kept..

But if you have TV out, I'd use the built in backup app, since that will let you restore to a repaired/new N900

Maybe do both, just to be on the safe side