Can you recommend some churches in Manila at which to hold baptisms?
All churches hold all types of sacred sacraments. The priests oath to serve 24/7 especially on the last rites. In case of baptism, most of the churches schedule it on weekends right after the misa cantada. Please note though that the arancel/fee may vary. You can also check this link for reference: http://www.smartparenting.com.ph/life/home/a-guide-to-baptism-packages-in-62-churches-parishes-in-metro-manila-2013-editionMagbasa pa
One of my nieces held her baptism in the church in Magallanes. Another one of my younger relatives had a baptism in the church in San Antonio plaza! You could check those out! Both ceremonies were beautiful.