Although I have no problem with either Atlantic or PTC I would suggest you go down to PTC and look at the set up. They are geared up to getting you through with the flying and exams. Then compare the two organisations, based on service, quality, and lastly cost. One may look more expensive, but if you look at the overall training programme, the most expensive may work out cheaper in the long run. Do a thorough check out of them first, and then lay out your plan, not their ideas, but what you think is a realistic plan, and cost it out.
With regard to PTC they have a well amitained fleet of aircraft with on-site maintainence which is a bonus when it comes to your tech-type exams as the engineers are happy to help you with questions
The other thing to consider is the continuity of flying, as in Cork there are numerous occassions when ATC limit training flights, whereas in Waterford you have very little interuption, this is costly during training. Landing fees at Cork and Waterford are fairly similar.
Weather is another major consideration as people have found out. Cork being 500 AMSL is frequently unsuitable for flight training due to low cloud and fog. Waterford being lower have a better weather pattern.
Take your time before deciding