It seems like the way manuscripts works with paragraphs and sections is a bit counter intuitive. It would make the most sense if you could select multiple paragraphs and then you could right click and select, "make new subsection from selection." It would also make sense if you could drag multiple paragraphs at the same time to organize them.
As it stands the only way to make a new subsection within an existing section is to create an empty subsection and then drag each paragraph there individually. There should really be a way to drag several paragraphs at the same time.
Let me know if I'm missing something or if there is a way to accomplish this that I'm not seeing.