If it's just you, the wife, and two kids, I think transporation will be fairly easy as long as you are willing to pay for private transfer to/from airports. All the resorts will be able to arrange a comfy van that would fit all your gear and kids safely...
If you have to fly and transit in Manila, it can help a little to use PAL (Philippine Airlines) for both the international leg and the domestic legs as their int'l and domestic flights share the same terminal.
But if your destination is in the Cebu region, best to just fly into Cebu. Not sure where in Europe you are flying from, but a lot of people prefer to fly from Europe to Hong Kong and then transit directly to Cebu, bypassing Manila. However, if you plan on going straight to Bohol, maybe it's better to fly into Manila and then fly to Bohol (Tagbilaran)
Quick question, and the answer might influence where you decide on. How are your kids with long car rides? 1hr? 2hr? 4hrs?
PG: you're looking at 2-2 1/2hrs from the airport to the boat pickup in Batangas + 1hr boat ride.
Malapascua - you're looking at 3 1/2-4hrs in the car (can get quite bumpy on the last leg) plus 1/2hr boat ride.
Panglao - whether you arrive by Fast catamaran ferry from Cebu or from Tagbilaran Airport, it's just a quick 30-40 min ride to the resorts down on Alona Beach. If you don't mind being stuck in a single resort, consider Bohol Beach Club. It's further north of Alona Beach so it's not walking distance from the restaurants and dive shops on Alona. But it has nice facilities including one of the best white sand beaches on Panglao island, very nice pool, and has numurous detached bungalows which would be great for a family. There's a small dive shop on the premises as well. Nice DM's. I was lucky enough to have the entire bangka to myself for a couple days one summer. Great drop off right in front of the resort and they will go to Balicasag and other dive spots.
As Drew mentioned, Alona Palms is another higher end resort that comes well recommended. And you're right in Alona Beach, so you can walk down and have access to a variety of restaurants. Nice pool and rooms there. Rooms are set back from the beach so it's pretty quiet.
Unless you like roughing it, I wouldn't consider staying on Balicasag Island. And really, it's just a quick 30min ride from Alona Beach. But don't miss out on diving it. Beautiful little white sand fringed island with some very interesting diving. (don't forget to look around in the shallows for interesting macro critters!).
Dumaguete - I've only stayed at Atlantis. Nice cozy place, great staff, and good food. They do have a small shallow pool towards the back. Black volcanic beaches but interesting place for walking along the shore.