The easiest way would probably be to find yourself a photo of a Spitfire you like and pick the configuration from that one. I have however tried to answer your questions below and I hope that clears things a bit!
This page might offer some inspiration by the way!
is ok to use the wing mounted bombs and the centrally mounted bombs together or is it one or the other?
No, I don't think so. I am almost sure it is either/or! what would a correct gun/cannon configuration be for having bombs mounted?
Depends on how the aircraft was built, with a C-wing or an E-wing. For D-day I would go for C-wing! When would it have the bump mounted in the centre (D13)?
I don't have the ICM kit but if the bump is a slipper tank, I would say likely not when in combat! when would it have the air intake on the underside of the nose (D7,D8,D9) and when would it have the intake on the under side of the wings (D11,D12)
There is always an intake below the nose but there
were different types of intakes. As for the wings: always! when would it have the rounded (D5) or pointy tail (D6)?
Pointy tail is for late build machines, D-day - typically rounded I would say! when would it have the rounded (E9) or flat (E7) wing tips?
Depends on if it was specifically built for low altitude operations.
Typical gun/cannon arrangement of a C-wing!
Photo showing slipper tank and short nose intake.

You could pick this as your "typical D-day Spitfire":
C-wing
No slipper tank
Long under nose intake
Rounded tail
Rounded wing tips
Good luck!
Magnus