Long before the study period began, The Philippines were colonized by Austronesian seafarers from Taiwan. They apparently had exclusive control of the Philippines throughout the first millennium CE, however they traded extensively with Indonesia, Malaysia, China, and India, adopting Hindu and Buddhist customs. Thus, the slow percolation of genes along these trade routs was omnipresent.
1212: Refugees from political strife in Borneo arrive in the Visayas islands (Negros, Panay, Cebu, Bohol, and Leyte). If your ancestors were in Visayas in 1490, their ancestors could also have lived in Borneo in CE 1000.
1565: Following visit by Spanish explorers (notably Magellan) the Philippines were organized as a Spanish colony. The Spanish primarily used the city of Manila as a transshipment point in their transpacific trade with China. The Spanish administrators typically interacted with native Philippine aristocrats, and there seems to have been little intermarriage. (Check your family folklore.) During this time a Chinese merchant colony appeared in Manila, but again, there is little evidence of widespread intermarriage.
1898: The Spanish - American war ejected the Spanish to see them replaced by American administrators. The relationship with native Filipinos was not friendly as American dominance frustrated their desire for independence. The result as a protracted guerrilla war between Philippine partisans and the US army in which up to 200,000 civilians are thought to have perished. Your family history should clue you in as to whether you have American ancestors.