Also, if this big section had small sections at both sides instead of one, how would you read it then? Or what if the big section was on the right side?
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Manga are usually published in the same style as historical texts/long novels for Japanese and Chinese readers (I am a Chinese but ya, most of our readings nowadays are from left to right). For that reason, the flow of the structure is always from top to bottom, right to left. In the case where the page is split into 2 sections by an invisible (horizontal) line in the middle, It is always read from top to bottom of the upper section, then followed by top to bottom of the lower section.
Of course, some manga use slanted lines to guide the reader on which boxes to read next :)