If you are not a Fil-Am or do not have any Filipino ancestry, go to schools that are familiar with foreigners (so you will not stick out like a sore thumb). Fatima accepts a lot of foreigners and they have clerkship rotations in the US. There are rumors about problems with their US rotations but talk to them and clarify the situation. It may just be a minor problem. Angeles University Foundation also accepts foreigners (mostly Asians) but they do not have any US rotations. I heard Cebu Doctors University allow US rotations but you have to talk with their administrations. UERM also allow a lot of US rotations but they have a quota on foreign students (about 10% of class) plus almost all of them are Fil-Ams.
Most Filipino schools will allow you to take 1-2 months of rotation (some only electives) in the US.
For local Filipinos and Fil-Ams, the popular ones with good reputation are UST-FMS,FEU-NRMF, St. Luke's (they have a modern JCIA-accredited hospital-only 1 of 2 in Asia) or even DLSU-HSC. It's really not that important which school you go to as long as you prepare well for USMLE as all of these schools are well-established institutions.