Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Philippines to Cuba as you normally would.
These are just IATA (International Air Transport Association) codes. They are used in aviation to identify and differentiate airports. That’s why a Manila Ninoy Aquino Intl Airport to Havana Jose Marti Intl Airport flight would often be abbreviated as a MNL to HAV flight. While you’re still figuring out your travel plans, it’s not a bad idea to learn the names and codes of other airports around these areas: Las Tunas Airport (VTU), Holguín Frank Pais Airport (HOG), Baracoa Airport (BCA), Cienfuegos Airport (CFG), Santa Clara Airport (SNU).