"How do you BUILD and SYNCHRONIZE the Junction Tables?!"
With PHP coding.
You add a new article to the Articles table.
And then your PHP code automatically shows you a list of sections (maybe a set of checkboxes) and you check all the sections you want that article to be in.
And then the PHP code shows you each section you picked and, under each, a list of available subsections. Again, you check all the subsections you want the article in.
And you are done.