Another vote for Filezilla! Too bad I didn’t find that before paying for BulletProof… which now collects dust.
As already stated, you got the location right: domain.com
You can also create other directories in your /home/username/ space if you want a place for files that you don’t want accessed by the web.
Save up to $96 at Dreamhost with ALMOST97 promo code (I get $1).
Or save $97 with THEFULL97.