You'll want to keep your Pacific fleet together and send everything else to support an attack on the pirates. Hopefully by the time you get their islands (5-10 turns in) you can be in position to grab a lot of the trade slots before you end up at war with other Europeans.

This is also a big game changer in how you have to handle India, whereas prior once you had made a landing you were basically safe, now you will need to destroy whichever faction's port provinces ASAP.