I have flown out of Logan with pistols the last two years at Christmas both times went smoothly (American if it matters).
In my case, the pistols were in a Pelican 1170 case inside my normal soft side luggage. I was not bringing any ammo.
The Pelican case was secured with a non-TSA padlock and to the frame of my regular luggage with aircraft cable.
You can't use the self-serve kiosks, so find the line for exceptions. When it is your turn, tell the agent that you need to declare that you are traveling with unloaded firearms.
The agent should produce a little card that they sign and date, you sign and date, and in my case I taped to the outside of the Pelican case. If your firearms are in their own luggage, not nested like mine, then the card goes inside the case. The point is that there should be nothing on the outside of the luggage that indicates "firearms", but the card should be around so if TSA goes digging they know you weren't trying to pull a fast one.
My first time, the agent wanted to see the firearm, but didn't want to get within three feet of it. I opened the Pelican case, they looked, I closed and locked it with my non-TSA lock, taped the card to the case, zipped up my luggage, and we were all done. The agent then tagged it to be picked up at the baggage office and off it went. At my destination, it came out on the conveyor anyway. No issues.
On my return trip, it was largely the same, but this time the agent wanted to see that it was unloaded. I sort of looked at him for a second because I really didn't want to start handling a pistol at the ticket counter of an airport, so I said, "It has a chamber flag in it and no magazine". That was good enough. Same thing, as before, lock up case, sign card, stick card on case, zip up, and over to TSA. At this airport, I moved the bag to the TSA area and stood there until it was cleared. The baggage screener was telling me I didn't need to wait... then my bag went through and they just looked at me, smiled and gave a thumbs up. Off I go.
My second time at Logan was a bit different. I get to the counter, make my declaration, and the agent then tells me not to touch the bag. Ok... They sign the card, I sign the card, I am told to just slip it into the luggage through the zipper. Ok, I do so, and the bag gets tagged to go to the luggage office and off it goes. Odd, but easy. This time I had to pick the bag up at the luggage office.
That return trip went just like the first return trip. No problems, no special tagging, and I retrieved my bags from the conveyor.
I bring a spare non-TSA lock in my carry on luggage in case TSA for some reason cuts off my non-TSA lock. There are some who travel with firearms more than I do that have had it happen. I try to make a note of who the ticket agent is when I sign my declaration just in case there is some sort of issue. If my luggage is open, I grab a photo with my phone of the locked Pelican case with the declaration on it, just in case. I also travel with a copy of the TSA regulations and the Airline policy, just in case. I have never had occasion to use any of this extra stuff.
It really hasn't been much of an issue at all. Half of the time I was through the ticket/baggage line faster than if I didn't have a firearm with me. Know the procedure, know what you are and are not supposed to do, and all will go well.