Just to complete the answers, many other files actually sit in the icloud drive but hidden. That is on top of the directory mention mentioned for some files as stated above. In particular, all PDFs are stored hiddend.
These days you can send things to icloud drive under different apps but Apple not telling you where it is.
If you do not want to go through terminal (and use ls -al etc.) try this:
- copy a named pdf say "a=pdf.pdf" to ibook
- search for a=pdf.pdf
if there is no such second copy,
try this further
add pdf as a kind into the search field (whatever the search is)
search for "a" instead of "a=pdf.pdf" (or any other possible filename)
your file would appear (as the original copy)
click the open the enclosing folder
It works in El Captain just a moment ago.