Well, I think I am pretty happy with my PEQ results, or at least got it as good as my Audyssey multi eq unit could. This time I did as Neil suggested, I kept Audyssey and the PEQ seperate. I had tried boosting the LF a little on my last attempt, but over time it became quite apparent this was not working, so I have left the Sub pro alone to do what it does best.
I spent all day yesterday swapping back and forth, PEQ then Audyssey 'multi' EQ, I can say there was hardly anything between the two, to a point where I removed the Audyssey unit from circuit as I felt I could not hear any change when using the 'bypass' on/off switch on the front of the multi EQ, it was that close. I did come to the conclusion, if anything there was slightly more bass with Audyssey. 'I was only testing 80hz up'
So I have decided I may as well put my multi eq unit up for sale. If you can not be bothered using the PEQ, then this could be for you.