You have a limit to how much Kamui you can 'store up'. When the bar is full, you are 'wasting' Kamui. This is not to say that you should pop it immediately, but don't run around forever waiting for the perfect time to use it. The bar fills up really quickly, so use it often. When I play, whenever I have 3 or more enemies around me and a full Kamui bar, I usually use it. There are exceptions to this rule, when you know (or feel) you are about to run into a boss fight or have just died trying to go through a tough section, store up the Kamui prior to the ugliness and make your life easier. Another thing to note about Kamui, it is character independent, meaning that each of your four characters can all have full Kamui. So if you have a really, really bad fight, store up or use items to cap off all four characters and then use Kamui from each in succession.