There are a number of reasons why the Spanish left Cebu and went north to Manila.  Among them are:

• Trouble in Cebu.  Legazpi and the other Spaniards faced problems with the Filipinos in Cebu.  There had been cultural misunderstandings and other conflicts and the relationship was breaking down.
• Threat of the Portuguese.  The Portuguese claimed the region and would attack the Spaniards.  These attacks made the Spanish feel insecure in Cebu.
• What they had heard about Manila.  They heard that Manila was a rich place with a good harbor that could be easily defended.  These atttributes made it seem appealing to them.