As mentioned in the comments, the 6 yellow SATA ports are on your Raid Controller (you probably need to set it to RAID mode in the BIOS if it isn't already).
The two purple connectors are for the other controller. Use this for a DVD-RW drive, etc.
My recommendation for you is to avoid RAID0 completely. Striping data is asking for trouble if the data is of ANY significance to your organisation. A single disk failure in a stripe results in complete loss of all data. I'm yet to work in any organisation where any data loss is considered acceptable.
If the only drives you have available are the drives you mentioned, I'd suggest using the two smaller drivers in RAID1 and install your OS on that. Then use the two larger drives in RAID1 and use that to store your data.
This setup will allow you to continue functioning in the event of a single hard drive failure on either array.
However, if the combined space available when in RAID 1 is not enough for your needs, A more ideal setup would be to use either of the two drive sets you have in RAID1 for the OS (probably the 500gb drives as I'd imagine they would be newer) and install the OS on that. Then get 4x brand new drives (3TB if you can) and put them in RAID 10 (6TB accessible), or RAID5 (9TB accessible) on the remaining 4 ports. Put your data on that.
You could even simply buy 2x 3TB drives and put in RAID1. Halving your costs.
Hope this helps.