For what it’s worth, EagleFiler is designed so that the top-level folder is the holding folder. You can see all the unprocessed files under the Unfiled smart folder, and they will also be tagged as “unread”.
Yes, if you hold down the Option key, EagleFiler will prompt you for a folder (which it will remember between launches).
You could also create an AppleScript (saved as a application) that imports into a particular folder and use that instead of “Save PDF to EagleFiler”. For example, this script:
on open _files
tell application "EagleFiler"
tell library document 1
set _folder to library record "holding folder" of root folder
import files _files container _folder
Thank you for these comments, and for the AppleScript. These are exactly what I was hoping to learn! I had not discovered the “Unfiled” tag, and this gives me exactly what I was looking for. Thanks again.