You'll be able to apply your NE2 credit to whatever the price of the phone is based on the contract term you agree to.
If you have a $50 NE2 credit and sign a new two year contract, you will pay $249 - $50 = $199.
That's assuming, of course, that your NE2 credit is worth $50 and that the speculated $249 price is correct. My NE2 comes up on Wednesday but is only worth $30 off.
Don't quote me on this, but I believe if you spend over $79.99 a month for a calling plan you get a $50 credit, if you spend less than that your credit will be worth $30.
This is assuming that your NE2 credit became available recently; some people who have not upgraded their phone over the last two years or so may have a $100 credit.
If you sign into your account on the VZW website you should see your NE2 eligibility there. If you don't see an actual dollar amount, go through the Upgrade Your Phone prompts until you see the list of available phones; I believe the credit will appear on the right side of the page with any other discounts available on the phones, like the 2-year contract price. If it doesn't show up there then follow the advice above and call VZW to find out.