The iCloud Drive connection that you create in iAnnotate is only able to show files that are associated with iAnnotate. So, the only files you'll see in that folder are files you saved to iCloud from within iAnnotate.
However, you can import a document from any iCloud folder. To do this start from the main library in iAnnotate --> tap the orange plus sign at the bottom of the screen ---> tap "Import File", you'll see a popup view of your different folders in iCloud --> navigate to the folder and select the file you'd like to work with.
