Have you ever used "du" from the command line? Man it if you need the full parameter list. I used "du -h -s *" to give me subtotals by each direct subdirectory of the directory I'm in (and -h for "human readable").
I've never used it for checking my closeness to my plan limits, but you should note that it will list the size regardless of user and I think the dhapache files are not counted against you.
BTW, regarding how often the monitoring runs, I remember reading that it ran daily, but I'd swear that it runs less often that that.
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