I ended up doing a HW RAID 0. The machines I am working with had that built in. The data on the 6TB RAID 0 is disposable, so no problems there.
Here is the first draft at my first custom config:
SSD has / across the entire disk
No swap file as we have 60GB of ram in this machine.
HW RAID 0 6TB
Reasoning behind this config is that the OS & SW (MATLAB & Synergy) will be loaded on the SSD drive for speed. /var, /tmp on the TB drive due to /var/log file always graowing and slowing the SSD down if placed there. /tmp on the TB drive as I have read that the /tmp file tends to shorten the life of the SSD drives and /home on the TB as the data generated by MATLAB is huge but disposable.
Let me know. My main concern is the size I chose for /var and /tmp. After reading this link http://www.tldp.org/LDP/intro-linux/...ect_03_01.html
it mentioned the entire size of / was 100-500MB, so I guessed that 1GB should suffice for /var and /tmp.
Thanks to all members for your support!