Do it like this:
price for the jeep standard invoice less 1-2% (invoice prices in the 2013 sticky at the top)
then for the hail damage
less 900 for a new hood
JK Heat Reduction Hood - Hood / Snorkels - Body / Exterior - Shop By Category
+ 100 dollars shipping
edit: looks like the sticky became unstuck
invoice price is in brackets
+ 500 for factory matching paint
+ 100 dollars for you your time and effort
so hail damage = 1600 off. Round it off to 2000 since it will never be exact and come resale/trade in down the road it will surely be marked somewhere as a hail damaged vehicle.
So cost of vehicle: invoice less 1-2%, hail damage discount: $2000
Spell it out to them like the above and see what they say.
Provided this damage is only on the hood. Inspect it thoroughly everywhere, even if there is one dent anywhere else.