Hi Supun,
the stackup that you put in HL or in PCB has to come from a Pcb manufacturer, or must have been validated by it. Otherwise you can "invent" a stackup that is not manufacturable.
For simulation always use the best possible stackup, that is most exact to the stackup that the board will be made of.
For manufacturing the stackup should be the exact rappresentation that you got from the PCB manufacturer.
For PCB you use an approximation, that is still relevant to the simulation stackup.
Hope this helps
Matija