I've used them at Malapascua and Dumaguette. Agree that Ricco is their best man at Dumaguette. I can also say that Atlantis is just as competent and well run. Can't go wrong with either. Both are very clean but out of town so you'll have to eat at either places most times. I prefer the rooms in Atlantis a little more for personal reasons.
However will not say the same for the SE ops in Malapascua. They use the Cocobana resort which is clean and on the beach. No A/C but mosquito nets and the rooms were cleaned daily. It is located right in the center of the main beach so it's very convenient, not that there's a lot to do on Malapascua (nor is it very big)
Their dive boats are slower and usually more packed to the brim. They didn't do calangaman island often because of the slower boats. Lastly, their dive guides tend not to rein in errant divers, especially on Monad Shoal where the threshers are. They allowed people to chase sharks for photo/video and ruining opportunities for others. I spoke with them about that but it still happened so I jumped to another ops, Bubble07.
Bubble07 on Malapascua is brit run but they have a fast boat and often very competitive prices. I normally go to local run dive ops vs foreign owned ones but Malapascua is one of those places I want a faster boat. You only do 3-4 dives aday. They also had a great marine biologist student who has the same enthusiasm as a new diver when looking for critters. We found winged pipefish, Hippocampus Denise and other small and wonderful things. He is unfortunately no longer there. Bubble07 also does tech dives on the WWII wreck, quite interesting when the viz is good. He has twins setups available.
The SE Bohol setup is also decent looking but I've never used them there so I can't say. I will say Bohol is a nice place to dive and quite fishy, although it's not top class but worth it for a few days at least.