Road Cycling - Stem issue

Hi all, just a quick question about bike set up for all you more experiences guys and girls out there.
My LBS supplied my new Cannondale with the stem flipped to the more upright position. Now wanting to tweak my position a little I have decided to turn it over to the flat position. ( I think it looks better as well ). My concern is that when a flippable stem is turned over then does it increase the effective length ?, my calculations say it does. If I find myself too stretched can I counterbalance this with moving the saddle a little further forward, (how does this affect the riding dynamics ?)

Thanks

Saddle position will effect your position over the bottom bracket as well as over the pedals so be careful about playing with that. Ideally, you should get that position correct first and then determine your stem reach... not the other way around.

This chart (http://www.habcycles.com/fitting.html) has always helped me visualise things...

http://www.habcycles.com/stemfit.jpg

What is the correct positioning of saddle over BB, Is it an entirely personal thing ? or is there a correct theory behind the position it ?

It has more to do with making sure that your knees are correctly positioned. When the pedal is at the front of its rotation (3 o'clock on the right pedal), the small bony bump right below your kneecap should be even with the axle of the pedal. Once you have set the saddle height and this fore/aft positioning, then you move on to the front end of the bike.

It depends on the stem. I had a Cannondale stock stem that was mesured from the upright position as a 110mm. When flipped flat it increased the distance to about 117mm. Eventually, I ended up replacing it for a Cinelli.