Whiptail will send out two different waves, Tidal Waves and Small Waves. You do not have to avoid these waves; simply holdL1 and press the TRIANGLE for the Small Waves, and Square for the Tidal Waves. You should slice through the waves and be able to charge her.
You can revisit any stage in the game once completed, which is an excellent way to seek out a full gauge on any stage you hadn't yet achieved on one. What's more, any emblem you've managed to unlock (there are three per stage) will remain unlocked, as long as you complete the stage. However, you must build the meter up from scratch if you want to unlock any emblem you've yet to get on any stage, regardless if one or two are already unlocked.
Nariko Perform consecutive hits on enemies to build the combo counter on the left side of the gauge up as much as possible. If she gets injured or doesn't land a successful hit for a few seconds, the number will reset.
Kai You must also score consecutive hits as well. Building up the gauge is made considerably easier since her time constraints between hits are much more lax. Also, her use of aftertouch (when shooting arrows) allows you to guide the arrow to its intended target.