The first is most commonly used. But for the second, it feels that the statement is incomplete, unless you change the word to clearer. "I need to make my points to you clearer" or "I need to make my points to you clear enough for you to understand."

The position of "to you" affects the meaning. "I need to make my points to you clear" implies the points are directed to "you" only. "I need to make my points clear to you" indicates the points are not specific to "you", but the effort to make them clear is.

I guess both are okey what only changes is the place where you put "Clear"