Hi @fp99,
You don't need to do anything particularly different.
We have a demo for the Pmod VGA on the Zybo Z7 that uses two differential Pmod ports on the Zybo Z7 (https://reference.digilentinc.com/learn/programmable-logic/tutorials/zybo-z7-pmod-vga-demo/start) and looking at the .xdc for the project (https://github.com/Digilent/Zybo-Z7-20-Pmod-VGA/blob/master/src/constraints/Zybo-Z7-Master.xdc) there is not anything fancy done for those differential ports, just the normal naming of the pins to match the name of the signal used in the design.
Thanks,
JColvin
