I can see my external drive in PC Man File Manager
ok, highlight the drive and click Alt+Return, or File, File prperties from the PCMan menu bar. Note the location, probably /media, and the filename, possibly sda#, so the drive is mounted on /media/sda# (ie sda1). That is where you want Photorec to save your files.

but can't seem to change the read/write permissions
On the PCMAn dialogue that opened when you highlighted the drive, you will see a permissions tab, try changing them there and see if it works. You can also try entering a command in a root shell.
Code:
chmod -R 777 /media/sda#
.

I know that some people have had issues with MyBooks in linux, and I havent had any experience with one myself.

Be forwarned that some users believe that writing to NTFS formatted drives is not safe with Knoppix, I tend to avoid it. I don't know how the WD drives come formatted.