Giving youself 1/2-full day for transfers between locations, I think 2 full weeks is plenty of time to enjoy all three locations without feeling rushed. I think 3-4 days in Alona/ Dumaguete is fine.
I did something similiar last year, although it was about 1 & 1/2 weeks. I flew into Bohol (via Manila) and spent about 3 days in Alona (diving along Panglao Island and Balicasag), then transferred to Dumaguete (Dauin) and did 3-4 days there (including a day trip to Apo Island). Then took the ferry back to Cebu, stayed in Cebu City overnite and then headed out to Malapascua for about 2+1/2 days. Then finally back to Cebu for a flight home.
I guess it really depends on the person. I'm the opposite of my European friends who prefer to stay in 1 location for 1-2 weeks. I usually prefer to hop around but still give myself enough time to appreciate the different locations.
To save on some time backtracking, you could consider the option of flying into Manila. Then you could
1)catch a connecting flight to Tacloban (Leyte) Both PAL and Cebu Pacific have flights to Leyte
2) Dive at Sogod Bay
3) take a morning ferry back to Cebu and catch the afternoon ferry to Tagbilaran (Bohol)
4) Dive in Alona/ Balicasag
5) Take the Tagbilaran (Bohol) ferry to Dumaguete
6) Dive Dauin and Apo Island
7) Hop on a flight from Dumaguete to Manila*
*usually the flights back to Manila are early morning so you should have enough time for an afternoon int'l connection.