In order to have calibre automount the reader you'll have to recompile the kernel without support for older SYSFS. Check this question in the calibre faq for more info.
http://calibre-ebook.com/user_manual/faq.html#id25
If you just want to mount it manually then type 'fdisk -l' as root (or with sudo), find the device on the list and then mount it to any point you want with 'mount /dev/sdx /media/reader' (/dev/sdx is the partition of your device) as root. the folowing: