Nature Communications and Nature subject journal differences from Nature
It's weird to me that this question has no answers even though it is a bit old now. I have a friend in STEM who talks about these journals in a way that seems fairly straightforward to me. 


A publication in Nature itself is obviously the most prestigious and is roughly equivalent with publishing in the most respected journal in your field.
Nature subject journals are a tier below Nature, but are also extremely prestigious and can allow young PhD students and postdocs to break into permanent research positions.
Nature Communications is a respectable "megajournal" a tier below the subject journals. It accepts a larger number of publications.
Scientific Reports accepts a very large number of publications and most any good science can be published there. Its impact factor is half of Nature Communications.


Generally you only submit to one of these tiers, and if you are a student your advisor would be able to tell you which is the correct one to aim for.

Again, I don't do STEM research and this is based purely on the way my friend talks about these journals. If this is wrong or too judgmental please post a comment.