How can I set the pad spacing and size of the footprint of the PQFP package?
You use the nominal value for the pitch.  For most modern parts with anything finer than 50 mil pitch, you usually make the pad and space width the same.

You should use the worst case for both ends of the other dimension.  There is no point leaving extra space on the inside end of the pad under the IC.  I usually add about 20 mil (&frac12; mm) to the outside ends of the pads if manual soldering is going to be used.  It also helps with rework and placing scope probes.  It doesn't hurt with reflow soldering as long as the extra area is symmetric, and the surface tension therefore won't pull the package off its footprint when the solder is molten.