Our dog has been to Europe twice; actually she was born in St. Avold. We've never had any real problems with bringing her to the States and back, although the last time we flew from Germany to the US, the airline ticket counter gave us some grief about the carrier, even though this was an approved carrier. We made sure she had her rabies shot 30 days prior to flight and the proper health certificate.
We didn't have to go through the chip route because Fluffy came to us with an ear tatoo; so I can't help you with that. It was an either chip or tatoo policy. She also flies with us in the cabin, under the seat. Of course, your dogs are a bit big for that but do check out the approved carrier requirements, to avoid hassles.
Lufthansa has the best reputation for pets and has the largest space allowance. For this reason, we're flying into Frankfurt and driving to the South of France, but this may not be a solution for you.
One thing to watch is flying in the summer time. Some airlines will not ship pets in the summer. If the aircraft is delayed and stuck on the tarmac, the temperature in the cargo hold can be lethal. Good Luck.