Yes, you can add it to the second data port on the controller, BUT the PERC 6 does not support non-RAID, so you will need to create a single-disk RAID 0 with that disk.   You mean it can't be seen at all by the system? or the PERC can't use the disk installed there? It absolutely cannot be managed by the PERC installed there.
I have a PE T300 and id like to use the cdrom sata/power cable to install a 5th hard drive (independent non-raid). Can this be done?
PE T300 Replace CDROM with SSD