Areca Cards
So my set up with the previous generation 1882ix was:
Four 1TB Crucial M500s on each of the MPs original bays, four 1TB Crucial M500s on a DX4 carrier (
http://www.transintl.com/dx4-for-mac-pro-2009-2010-no-drives.html) and two 1TB M500s on the 2nd empty optical bay.
The drives on the optical bay are actually my boot drive and VM drives -- I don't use bootcamp, but I assume you could set up one of your drives to boot OSX and the other your bootcamp partition. The eight 1TB drives on the standard bays and DX4 are all set up as a RAID 1+0. I am slightly paranoid about data loss, and my Areca 1882ix card also has one external port to which I have hooked up an external RAID 1+0 hard drive array. This external RAID array I use as a backup and it can also be booted from.
The only thing you have to be aware of when you set up these arrays is that the logical drives cannot be greater than 2TB if you expect to be able to boot from them. I didn't have this problem with my Promise R6 array connected to my iMac, but this Areca card does not seem to support larger than 2TB boot drives.
As to your question, the HDD drive bays will support whatever speed your RAID card supports (so yes, it will support 6gbps throughput).
I am not sure what you are using your computer for, but with this set up you will definitely have a computer with very little I/O bottlenecks.
I should say that money was not so much a concern on my end -- this server was built for my office -- speed and reliability were the primary concerns.