Selected Moalboal as I wanted to be on Cebu Island before our flight out. Was thinking the sardine school would be cool and Pescador island would be nice diving and then maybe a trip to the waterfall on the last day.
We're traveling in February
You don't need to stay on Cebu before your flight esp. in feb (Low probability of weather issues). Dauin-Mactan can be done by private van/ferry.
I can understand you'd like to see the Sardines school (and Pescador walls) however the sardines school is overpopulated with daytrip snorkelers starting from 10 AM, plus the water gets really sh*ttier (for real!) later in the day, hence I would advise you to dive it as early as you can, depending on where it moved on Panagsama it can be done from the shore (Last time I dived it you could start in front of Savedra or Nelson's).
Hence I recommend you should base yourself with a dive center on Panagsama and not away to southern based resorts like Magic island nor Turtle bay resort (Stayed there twice, they are neighbors to Magic island, didn't like their dive center, no flexibility at all, they were kind of secluded so I prefered to take a trike to Panagsama every morning but that's not practical at all) .
On my first stay in Moalboal a long time ago I stayed at Cabanas resort (I think now same owners by the italian restaurant), it was fine (esp. the breakfast mango pancakes) but I really don't know how it has evolved, probably aged a lot but the location cannot be better for the sardines (if the school didn't move in he past years).
My last stay was at Marcosas, which was OK a little south of the sardines action, just on front of the Quo Vadis resort, a 10 minutes walk from Panagsama "center".
A few years ago there were some accomodations buillding next to Cebu Fun Divers, 5 minutes walk from Nelson's may be these could be a solution for you.
There are now only very few dive center that will start early as 8AM, that's the best time for Pescador though. They're all starting aroud 10AM because they're waiting for the daytrippers and that's when Pescador gets INVADED with large Korean or Chinese groups. I'd suggest you start sending mails to the dive centers to check their schedule having in mind that the earlier in the morning the better for both visibility and avoiding large groups.
Talking about Dauin now : I have been diving with 4 different resorts and operations, Atlantis and Atmosphere get my votes for high end accomodations and grounds but Azure have the best guides I've seen in the area (owned by ex-Atlantis dive manager).
I have never been to Bongo Bongo but I see where they are located just on Marine Sanctuary entry (Sanctuary, or Cars dive spot). Apart from Apo island which is a divespot on its own, there are different areas to be dived from north to south.
San Miguel area (North close to Atlantis or Liquid) : very mucky Lembeh style area, black sand, cephalopods like blue rings, seaslugs and nudibranchs. A bit repetitive though.
Sanctuary area (Where you'll be located): more white sand macro dives, loooots of Ghostpipefish and small froggies. You will be a bit early in season. In april you can spot up to 10-12 of juvenile froggies per dive and a similar amount of GPF.
Masaplod area (closer to Azure or Atmosphere) : my favorite in Dauin, more variety small patches of reefs that attracts different species of nudibranches, frogfish, etc. probably an area that is more similar to Anilao diving in terms of variety.
Zamboanguita area, just in front of Apo (Southernest area, next to Thalatta resort) : quite deeper dive sites on white sand and artificial reefs with a very good variety as well, lots of cephalopods like Flamboyant cuttlefish in season, all kinds of shrimps like Harlequin. It's the furthest area for northern Dauin dive centers so they are sometimes reluctant to go, do insist to get there since it's very different from northern or central Dauin areas.
Now in terms of options in Feb. I am a big fan of Balicasag, it's one of the few areas where you can spot big schools of Jacks and Cudas, sometimes a whale shark, it's very easy to couple 2-3 dive days in Alona with Dauin : it only takes a 3 hours ferry ride from Tagbilaran to Dumaguete (hence you only lose the morning, you are in Dauin around midday.). Maybe you don't like traveling too much in 12 days but in my case I would do 2 days diving in Alona/Balicasag then transfer and 7 days in Dauin and ultimately 2 dive days in Moalboal which isn't worth more IMO.