I have two 500GTB 7.2k Sata 2.5in drives, plus twelve 2TB drives, and LSI 9260-8i SAS/SATA Card. I need to have OS on one label the rest for storage. I am unsure how to build the raid6. It has the LSI MegaRaid utility. Should I build it all as one array with raid 6? Then it asks if I want to add the array hole to the Span? What's the best way to handle this?
You say you have an LSI 8-port internal SAS card.
Unless you also have a SAS expander or enclosure (with an expander), you cannot connect 12 drives to an 8-port card...
If you are connecting these 12 drives to both the LSI card and onboard SATA connectors, you cannot use any kind of hardware RAID setup - use Linux softraid (mdraid) instead.
Assuming you can manage all these drives with your controller (and that assumption is not a sure thing), then don't build raids with differently sized (or speed) drives. Make a raid with the 2 500GB drives (raid 0 for striping, or 1 for mirroring), and a separate raid (or raids) with the 12 2TB drives.
If you are building raid 5 or 6, remember that the rebuild time on large drives is very long. And gets considerably worse if you're on raid 6 and suffer a double disk failure. Also, during this rebuild, you will suffer a lower performance for any normal IO done to the disk.
Two raid 5s with 6 disks each for your 2TB drives would lose you a bit of redundancy, where a double failure could cost you data if you were unlucky and both failures were on the same raid, but would allow you much better rebuild times.
Don't forget to account for a spare- ideally you would have a hot spare ready to swap in without waiting for a new drive, so your total available raidable 2TB drives would be 11, not 12.