Also remember that the "bass" and "treble" controls in Hijack will steal the top two bands of the equalizer if you use them. So if you're doing RTA and you intend to use the Hijack bass and treble controls, you need to leave the top two bands set at 0db.
I personally used the bottom 8 bands for RTA flattening, and now use the bass/treble controls for the overall "to taste" adjustment of my bass and treble. I'm quite happy with the way it's worked out.
Oh, and don't forget to kill the loudness setting before RTA'ing.