Where are you departing from Philippines?
I do not think there is direct flight from Puerto Princesa(PPS) to Dumaguete(DGT). Connection is through Cebu, Manila and others so it takes time. Check the flight schedules of both Cebu Pacific and Philippines Air Lines. Dumaguete is mainly from macro except on trip to Apo Island.
Puerto Galera is an nice all rounder but getting there by private transfer is ridiculously expensive.
Atlantis is over price.
This is better:
Welcome to Liquid Dive Resort, a small boutique resort located on a secluded beach front in Dauin, home to some of the best diving in the Philippines.
www.liquiddumaguete.com
If you really like macro then Anilao is highly recommended. And if weather turns foul then Manila is only few hrs away by car. June is the beginning of typhoon season so beware.
My suggestion is Malapascua. The beach is very nice.