Not booting after replacing the SuperDrive with SSD
I configured the SDD as the main startup disk and I transferred all
  the libraries in HDD.


How exactly did you transfer the libraries?!
Note, that Disk Utility.app (if used) does not create a bootable HDD backup!

There are different ways to clone/transfer the entire content of your previous installed main HDD. The following applications will allow exact and bootable drives/disk images.



Option 01: Carbon Cloner creates a bootable drive/volume





Option 02: CloneX4 allows you to make a bootable copy of your startup disk, as well as if you want to change your hard disk. Clone X will create a perfect bootable copy of your startup disk, or of any of your other disks. Clone X automatically handles all settings needed to make a correct bootable copy.