A friend recently visited Dumaguete and Atlantis and had glowing reports about both, especially the diving there. He worked in the Philippines for several years as an instructor so I trust his judgement.
The good thing about Dumaguete is you have access to Apo Island as well has the sites off Dumaguete itself. Atlantis sits on a nice black sand beach by itself according to him. He also said that the town has an upmarket, sophisticated night life due to the university located there so there are nice restaurants and bars should you decide to go into town.
I was in Bohol (Alona Beach) in August and thought the diving around Balicasag Island was excellent, we did two dives and saw a big school of barracuda on the first dive and a big school of jacks that spiralled up past us on the second. But I thought the other sites (the walls around Pangalao itself primarily) have good coral cover but not a lot of fish life. I'm not used to diving a lot of walls, and with the viz at 20+ mts I enjoyed hanging a bit off the wall and taking in the immensity of it all.
Alona Beach is very laid back and slow, which may be what you are looking for, and the beach is quite attractive. If you go to Bohol I recommend you dive with Genesis Divers located at Peter's House, ask for Eric Laurel. Peter's House is a cosy little guesthouse that is quite cheap if you are on a budget. If money is not an object then you could stay at Alona Palm next door, a very nice, new resort.
Drew