You can apply to any of the following Licensing offices in Manila:
1. Pasay City Licensing Center ( PCLC) - Domestic Road, Pasay City
2. San Juan Licensing Center - 108 Domingo St. San Juan City
3. Quezon City Licensing Center - LTO Main Compound, East Avenue, Quezon City
4. Manila Licensing Center - JT Centrale Mall, 1686 Fugoso St. Sta. Cruz, Manila
5. Kalookan Licensing Extension Office - Btel Bldg. Araneta Avenue, Kalookan City
6. Las Pinas Licensing Extension Office - FMC Compound, Alabang-Zapote Road, Talon 1, Las Pinas City
7. Taguig Licensing Extension Office - Old Admin Bldg. FTI Compound, Taguig City
8. Valenzuela Licensing Extension Office -ARCA Plaza, Maysan Road. Valenzuela City
Note that since August 3, there were changes in the processing of drivers permit. For licensing and renewal like yours, you can choose to go to any of the above mentioned places. It wont cost you much. I paid almost 1000 for non-professional application
Hope it helps.