The choice between that and it is entirely dependent on context - there are no rules, and guidelines are scarce. Paradoxically, misuse of that and it is one of the easiest ways to detect a non-native English speaker. It's just one of those things that you get. One could write pages on the subject, but we can address your specific examples in an attempt to give you a better idea of how these contexts are used.
In very general terms, one could say that that often refers to something more specific or quantifiable, while it often refers to something more vague or subjective.
I know [that/it].
I know that is a suitable response to a declarative statement, especially when confirming to the speaker that you do, indeed, know that. E.g., when my wife wants me to take out the trash, she could say "The trash comes on Wednesday," to which I would grumble and reply "I know that."
I know it is rare in written and spoken English. I've heard non-native speakers use the phrase as a substitute for "I am familiar with it" when referring to a place or landmark, which sounds a bit bizarre to native ears. Most often the phrase is followed by another clause, such as "I know it when I see it."
More often, native speakers will simply say I know.
What is [that/it)]?
What is that? is a very common question in English. It can be used when trying to identify an object you see someone holding in their hand or an object far in the distance. The important part is that you are almost always referring to something.
What is it? is also a relatively common question in English, and usually refers to something more abstract, like an idea or concept. "I've got something on my mind." "What is it?"
[That/It] is more than I wanted.
That is more than I wanted is similar to the example above. That often refers to something immediate or physical, such as if your friend poured too much wine into your glass.
It is more than I wanted often refers to an abstract idea, such as the outcome of an unwanted situation. "It is more than I wanted."
To know how you are, [that/it] is more important.
Not very common in English. One could argue that that is almost always used in a situation like this: a definite phrase is introduced, followed by a complete clause: "To be or not to be, that is the question."
Hopefully this helps to aid your decision making. Although tedious, perhaps the best way to learn the difference between that and it is to listen to native speakers and note the context in which they use one word in favor of the other.
The good news is that because the choice is so subjective, you stand very little chance of being misunderstood. Comprehension is the essence of communication, and unless you are writing literature, I wouldn't let it bother you too much.