iBooks management of PDF files
Usually the .pdf files can be only viewed in Safari without opening in iBooks, and this is as such since I remember, and this is default in any browser.
To save them, you have the option to &quot;open in iBooks&quot; and they will copied there, and the different Collection items is the only possibility to categorise them in iBooks.
But in Safari there are another possibility: from sharing symbol, choose &quot;Save to Files&quot; - and there you may create any number of folders, nested or not, as you wish/need.
The good news is you can move those .pdf files from iBooks: go Library -&gt; Collections -&gt; Edit and select the files you intend to move to Files and again, from sharing symbol choose &quot;Save to Files&quot; - then delete them from iBooks.