Okay, let's go over it a bit slower
AdminCP -> Usergroups -> Usergroup Manager -> Edit the usergroup you want (Administrators for your own account normally) -> DownloadsII Permissions -> Can Upload Images -> Yes -> Update
Now will you get the "upload an image" posssibility AFTER you added the file (the PDF in your case). The "upload an image" possibility is on the file page of it you get AFTER you clicked the Add-button for adding a file. It's located underneath the description like you see on
this screenshot.
The image(s) you upload, will be shown underneath that description on the file page
AND will be used as a thumb for the category view (this last thing is what you want, but this is not a separate upload thing, it's just using the standard images uploaded to a file AFTER you added it).
I hope that's enough information