What am I missing or misinterpreting here?
Maybe your guide is out of date. You surely don't need me to tell that it wouldn't be the first time.
My libraries are all in one folder. This can only be for one of two reasons:
1. I followed instructions - official or otherwise.
Or 2. I did the bleeding obvious.
and, guess what? It has never been a problem.
Further, if the OP has never downloaded a library before, and does the same, he/she is not likely to have a problem either.
And, in the unlikely event he has two "all the other libraries", either will do.
Maybe you are using an older IDE.......
Then maybe the OP is too. It isn't likely but, in that case, he has probably worked out what to do.