Issue with 2 Internal HDD Configuration (not SSD)

I have a 13" MacBook Pro mid 2012 with 500 GB HDD running Mavericks. Needing more space I bought a 1 TB Hitachi SATA 5400 RPM HDD and using a Caddy, replaced my Superdrive with the 1TB HDD. I have 2 partitions on the new HDD (0.5 TB each for Music and Photography) I intend to keep only OS and Documents on the Bootable Disk.

The problem I am facing is that the new HDD (both partitions) dissappear (ejected) aftter some time. The only way they will show up on my desktop or disk utility is on bootup. I would like them to be available all the time, or available to be mounted without booting up the notebook. I have searched the various forums with lots of solutions to use SSD + HDD configuration (eg.setting up a fusion drive etc). Nothing helpful on 2 HDDS. Help anyone?

Also, I am trying to move the iTunes Library to the Music Partition and store my Photos (to use with Lightroom) and iPhotos to the Photography partition, but still access them from the 'original' folder in my finder. Any advice on how to do this most effectively/efficiently?

Thank you.