I haven’t flown this route, but have flown EVA (among many others). It is almost always the case that if you really want to sit together and you care about your seats (do you mind sitting in the back of the plane?), you should pay for the seats you want. Doing so makes the question about when/where to check in moot, since you will have your seats already confirmed, but checking in online as soon as it’s available increases the chances that things will go smoothly. That said, if you purchased tickets together and are on one confirmation, you will PROBABLY be seated together. No guarantees, though, unless you pay for seats.