As a former airline agent in Boston, MA and having flown with my handgun from Milwaukee, it should not be a hassle at all. Here's the rundown of how you should do things.
First off, expect ignorance and perhaps shock.
Do not use an automated kiosk. You will need to talk to an airline agent.
The firearm must be in it's own, LOCKED, case. place the handgun in another bag.
You may carry a small amount of ammo, but it must be in a separate container, in factory packaging.
When you check in, simply state you need to declare a firearm. Depending on the agent, the airline, and the airport they might check it themselves, they might have a supervisor come over, or have tsa come over. In any case, they will want to see the firearm, have you sign that it is unloaded, and place the UNLOADED tag in the case with the firearm.
When I was flying out of MKE some months ago, the agent looked at my firearm, which was field stripped and was like "um...is it unloaded?" He had no idea what he was looking at.
After it has been checked by the airline, it will need to go to tsa for XRAY. sometimes they'll make you stand there while it is screened. ALWAYS make sure you tell TSA that there is a firearm in your luggage. Otherwise your bag may be delayed because they had to open it and gi through it and screen it more than once to verify that it is unloaded.
Just make sure you follow TSA and Airline rules for packaging, and always declare the firearm to the airline and tsa both.
As always, pack neatly and arrive with plenty of time for your bag to be screened. There is nothing worse than having a bag with your gun not make the flight in time.