BA does not take payment online.
You have to be there at least 2 hours before the flight.
You need shotgun cert plus EFP.....one for going out and the other for getting in Portugal.
You will have to complete a handling form at the check in (hope you get a check in desk who knows what they are doing).
If you get a thick one.....DO NOT....let them put the baggage tag around the handles or you will not be able to open case at customs. Take it with you and put on after customs. (Or if you get an arse...you will have to open the case and let them put it on one side of the handle only.)
Irritatingly....last time (may have changed now) but they do not take the money at the check in desk either....they send you off to a payment desk and you have to return with proof of payment before they finish with you. You are then accompanied the rest of the way through the exercise (customs then x-ray) by a specific person. You pay for out and in at one time (so keep the proof for the way back incase the gun check at Portuguese customs ask for it. I have seen the Italians charged again because they lost theirs).
At other end collect your suitcase and ask at the red/green channel where to collect you guns.
On way back from Portugal it is normally go to Police customs first and they seal your gun case with a numbered tag after checking ...then you go to BA and this time they can baggage tag your gun case....because it has been checked. You then get taken with it to a special load area (like for oversized baggage) where they take your gun case from you.
You never ever ever let it get put down the baggage chute with your suit case.
Hope that helps (it was description for Porto and some airports may alter slightly....just go with the flow. You can ask when you arrive at the other side....and get your guns....what the return procedure is....just to be on the safe side).
The easiest airline to fly guns is Easy Jet....by far.