That is for cancelling out feedback not eqing. When using the Parametric settings on the BFD it does not auto do anything and must be done manually, it's primary purpose was not to be used as a equalizer but to be used as a feedback destroyer which is does do automatically.
The only part of the qoute you put in your post on how to use the BFD's eq abilities
was
".....while the manual mode allows individual setting of up to 40 fully parametric filters with frequency, bandwidth and gain adjustment."
There was a good website that I got a link off AVS for setting up a BFD for a sub that I used when I got mine and it explained it all very cleary. I'll see if I can dig up a link, I'm sure it explains the auto part and why it's not relevant when using the Parametric EQ features better than I can.
Edit: heres the link
http://snapbug.tripod.com/