To set up both bikes so that your position over the cranks is the same, measure saddle height from the center of the crank (pedal if crank arms are different length) to the top of the saddle along a line that runs through the center of the seat tube, and measure the saddle set back parallel to the ground to a line that runs perpendicular to the ground from the tip of the saddle to where it intersects with the center of the crank.

Various road bike seat tube angles are not so so radically different that the height will be different by a significantly measurable amount. However, to be more precise mark the top of the saddle of the first bike you measure after it is setup to your fit. Mark the saddle of the other bike in the same place and measure height to that point.

Keep in in mind that bikes with different geometries may fit and feel different. So in the end, your best fit may be different on each bike.

Also, you may need to adjust for different saddles if the shapes and sizes are different.

Transferring fit measurements from one bike to a differently designed bike is probably best used as a starting guide and not necessarily as a final fit.

Good luck!