Unless you are really pressed for time, the first piece of "local knowledge" I can give is to wait till spring. Bashing into the NE Monsoon now, would be rather unpleasant.
If you want to make the Taiwanese officials happy you should let them know in advance that you are coming. The first post of call is Kaohsiung, but if you end up in Kenting (Houbihu marina) they will be able to process you, but the immigration office will have to come from Kaohsiung anyway. I have described the whole process for noonsite: Taiwan — Noonsite
But if you come unannounced, you'll be welcome too, with a little fuss maybe, depending who you run into
Currents can be quite strong (watch the tides carefully).
Not sure what is your destination
, but Kaohsiung is definitely a great place to stop. People are very welcoming. Contact Peter Pan (viz Noonsite) about a berth. He's usually able to find a place.
As for the trip itself, there's not too many options. Our last stop before leaving Philippines
for Hong Kong
was Bolinao. Last port of entry is San Fernando, never been there, perhaps others can comment on that. Only heard that it can be quite nasty (no protection).
Then it's a straight bash to Taiwan
Cmaps and Navionics
that we've seen) don't offer much detail for these parts
. If you are in Taiwan, that's easy. Otherwise I'm sure you'll be able to buy charts for Taiwan in PI as well.