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, if you select the orange plus sign at the bottom of the screen and tap "Import File", you'll see a popup view of your different folders in iCloud. To work with a file in iAnnotate, simply go to that folder and select the file you'd like to work with.