How many stitches did you have on each needle before the heel flap started? I have the book at home and can look up your specific pattern when I get home tonight. I think some of Cat Bordhi's socks are worked in profile as opposed to having the top of the foot on one needle and the heel on the other, and that may be adding to your confusion. Please post the pattern and page, and I'll look it up when I get home :-) I just cast on a new pair of socks from that book!
"Pinup Queen" by Annie Modesitt from Stitch N Bitch