The position of your saddle shouldn't be dictated by the position of your torso, upper body or arms - it's a function of how far forward your saddle is compared with your bottom bracket, the length of your legs, comfort of your legs and the muscles that you are using in your pedal stroke.
If you already have a suitable position on the saddle then the only change you'd want to make for clip-ons or a full TT bike would be to rotate your position around the bottom bracket, bringing your saddle both forward and higher. Doing so (guideline seems to be around 2mm height for each 10mm forward) would mean your torso also rotates around the bottom bracket, making your bars lower and (to a degree) closer. Since your relationship between saddle and bottom bracket remains the same, the pedalling dynamic remains (relatively) intact.
With clip-ons you have a great opportunity to try out different positions as you won't have to re-cable each time the aero bars are moved; experiment with the bars being narrow or wide, angle them horizontal (traditional), slightly up (pretty common) or very much up (preying mantis position) and if the elbow pads can be rotated or adjusted independently (Zipp Vuka, Profile Design T2/3/4, etc.) then do so; use positions outside at a reasonable pace as some positions seem fine at first but quickly show themselves as unusable when used in anger.
If your aim is to reduce your frontal area / CdA, remember that narrower can beat lower for some riders and that position needs to be a compromise between power output and aeroness - it's no good being low if you're slower because you can't use your power
