Incorrect Directory when Sending to Device

[Rattor]

I'm having an odd issue. I started my library collection on my Nook Color, and I recently upgraded to a Nook HD+. All I did was copy-paste the directory with my ebooks in it to the new SD card for the HD+.

My issue is twofold. First, Calibre is not recognizing that the books are already on the device, even though Calibre is set to scan the directory that the ebooks are in. Second, when I try to send a book to device, I have it set to send to My Files/Books/{author_sort}/{title}/{title} - {authors} on the memory card A. Instead, the books always go to Books/My Files/Books/{author_sort}/{title}/{title} - {authors}.

Is there a way for Calibre to recognize books already on the device, and is there a way to remove that initial Books directory from my send to device path?

Thanks for any help.

EDIT: While trying to setup my device, I came across another issue. On my Nook Color (and now HD+) I like to create shortcuts on my custom launcher home screens to books that I'm reading. To do this, I need a separate jpg file for the cover so that the icon I create will have the book cover on it. However, with MTP devices, you can no longer save to disc, which allowed me to save the cover as a separate jpg, and I can't figure out how to tweak send to device to allow the sending of a separate jpg for the cover. Any help here too?