seat height

Hi all, I am new to road cycling and have a Giant TCR Alliance Zero. I have been looking at this link below for adjusting seat height and am using the 109% method. The only thing is, I have done all the calculations and it comes in at 88.29cm. When I measure this from the axle as it says my seat is way to high - Do I need to take off the height from floor to axle? Any help would be greatly appreciated.
http://www.bikeradar.com/mtb/fitness/ar ... ight-14608
http://www.bikeradar.com/mtb/fitness/ar ... ight-14608
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Obviously you want to avoid hips swaying side to side (seat too high) or an overly bent knee (too low), but given my starting point method I can quickly get the best position based on feel and comfort.
That method has worked well for me.
http://farm4.static.flickr.com/3013/243 ... 8d.jpg?v=0
http://img362.imageshack.us/my.php?imag ... 076tl5.jpg
http://img216.imageshack.us/img216/3407 ... e001af.jpg
Have a look here http://bikedynamics.co.uk/page_1228826262495.html for fitting guidelines. It helps if you can measure angles though.