if I’ve mounted my Pixhawk 90 degrees clockwise(arrow head pointing rightwards) and configured it with the help of mission planner , then can I mount my GPS straight itself (arrow head pointing forward) or am I supposed to match its direction with Pixhawk?
You can mount them in nearly any orientation.
Use AHRS_ORIENTATION to account for the autopilot (probably a value of 4 in your case).
The GPS antenna itself has no orientation associated, but if there is a compass integrated into the module, use COMPASS_ORIENT to account for the mounting (probably a value of 0 if the arrow is forward). Be sure you adjust the correct COMPASS_ORIENTx parameter, since they are numbered if you have more than one.
COMPASS_AUTO_ROT if enabled, which it is by default, will take of the compass orientation during compass calibration. It’s worked well for me on Planes.