how to properly use "that that" so as a listener/reader/speaker can comprehend the entire sentence without complication?
Be it either whilst writing or reading, I've not come by an easy way to comprehend the use of the 'that that' lexical ambiguity, taking into account that improper use of punctuation is not the issue.
Is there an example anyone could cite (and link if possible) that doesn't affect the flow of the prose itself to the reader?
He said that that won't do.
I think that that is the best choice.
Oftentimes the problematic "that" is superfluous and can simply be removed (especially colloquially). For example, instead of "I think that that is the best choice," just say "I think that is the best choice."
Another option is to eliminate "I think that," and simply state the opinion that forms the most important part of the sentence: "That is the best choice." Oftentimes it is presumptively the case that what a speaker says is his own opinion. Of course, context may make this approach unsuitable (e.g., where the speaker is emphasizing that the opinion is his own).
There are plenty of other ways to restructure as well. "According to him, ..." instead of "He said that," for example.