This sense of "make" is like "cause" or "force. The form is : make + object + adjective e.g. The teacher made the test hard by reducing the time limit. Sometimes, you can't describe the object in one or two words because you are describing a more complex situation. In this case, you use "it" as the object to refer to the situation, then another clause which explains the situation. e.g. The teacher made it impossible for the students to cheat in the test. e.g. The teacher made it clear that cheating would not be permitted.

The phrase "make it" is idiomatic. It means to "to succeed in doing something" (ex. make it big - to become successful) or "succeed in surviving" - (make it through). "make clear" by itself is transitive, you will need a direct object. You can't say "I make clear.", you have to say "I make my intention clear", or "I make it clear". The same as "make obvious", you must say "I make the answer obvious" or "I make it obvious" Btw "How to make it obvious that you want a something else?" should be "How to make it obvious that you want something else?", no "a" before "something"