You can use *A miles to upgrade, but only from Y, B or K class fares, and only if your segments are unmarried (something only your travel agent or a live EVA sales agent can know or verify) or the fare breaks at TPE.

You can also use EVA miles to upgrade, but at the same rate as *A, and if your coach class is deeply discounted, it might require too many miles to be practical, or disallowed altogether.

A competent EVA specialist in Flushing will be able to handle this for you, just make sure your JFK-TPE segments are in Y, B or K class and make sure when they sell the fare, the segments are not married. If your dates are flexible, make sure you or the travel agent call EVA and look for Z class seats (never, ever tell them you want to use *A miles, just keep insisting on Z class seats or they make a fuss about not being able to check) before issuing the ticket, then you can call the *A carrier your miles are with to process the upgrade (United has an automated tool for this, other *A you need to call). A *A upgrade JFK-TPE-JFK (forget the Bali segment) is 30,000 *A miles each way.

If you want to use BR miles, then you need to open an account and find a credit card with enough points to transfer over.