It all depends whether you want to buy a house or rent it. In any case my advice will be to find a place in a flood free area. Avoid uptown as traffic is awesome during rush hours and driving from central area to uptown can take several hours. But Uptown has some advantages. During selection of a place you must consider your budget, where would you work, where would your child go to school etc. The last part will be important as your son is minor.
Regarding independent house or condo, I always prefer to have my own house. As I couldnt buy the lot in my name I have done some arrangements to safeguard my interest. So I put the building in my name and that way I can have some peace of mind. But having a house also means that you also need to have a security plan if the area doesn't have any prior common security arrangement. In my house I have a wonderful garden where I can sit in totally peaceful area of Nazareth, which is very central and flood free as far as my street is concerned.
As you are a filipino you dont have to safeguard your interest while buying a house. As you have never been to Cagayan de oro before, rent a small place which will be better. Remember that Cagayan de Oro is a third class city of Philippines and there is some risk due to problems with some muslim communities in the neighboring areas. Rent a small place in a flood free area and see whether you want to stay in this city. Make your budget and look to your priorities before moving out to a bigger house. It doesnt make any difference whether it is an apartment or condo to start with as long as it is a flood free area and you can live with traffic problems and pollution during rush time. Remember also that it can rain a lot in Cagayan de Oro during rainy season. and many house gets flooded. Many house owners will like to rent their house for minimum 12 months, so you can get stucked in a flood prone area for many months. The rent can be from 8000-10000 pesos a month; some of them are not worth to stay while others have some better standard specially if they are not located in area where there is lot of demand.
Regarding the school, I sent the child to Lourdes High School as it was very near. I paid around 38000 pesos a year and he learnt very little. This year I moved him to ANE which is also near to my house. The fee is 70000 pesos a year. Xavier costs something between these 2 schools. I wanted to admit the child to ANE as I wanted him to be more fluent in English language. Good luck!