A way to simplify things is to think of short phrases as if they were single words. "il y a" is an obvious example. With "j'ai" as a single word, one does not have to think about the rule were the terminating vowel of a word must be replaced with an apostrophe when the next word begins with a vowel. And with "ce qui est", one does not need to think about the rules about when to use "ce que" vs "ce qui".