With respect to the X11SSM-F SATA ports, I am using ESXi, meaning I run FreeNAS in a VM so i need to pass though ports which is why I have the add-on cards. I cannot do that with the motherboard ports, well not the way I want to. If you are running FreeNAS on bare metal then the SATA port on the motherboard are fine.
With respect to the RAID calculator...
Four 3TB hard drives in a RAIDZ2 configuration gives you 5.5TB of storage.
Reduce 5.5TB by 20% (5.5 minus 1.1) and you are down to 4.4TB of storage.
Reduce 2GB from each drive for the SWAP file which is automatically created, now you have ~4.4TB (minor difference but worth mentioning).
The 20% reduction is so you never exceed 80% full. When you exceed 80% full then the file operation slow down a bit. The real slow down occurs at 90% full where the file system switches into a write optimization mode and you will notice it. Now if you are only watching movies on your syste, exceeding the 80% rule is not an issue, but the 90% value will likely be an issue. Backing up a bit, the 80% rule is basically, so long as you are under 80% then your pool is considered healthy. I promote the 80% rule because if someone hits that, odds are they will get to 90% and things slow down and they will create a posting asking why the system slowed down. They forget about this 90% write optimization mode.
I hope that clears things up.
So if you have six 3TB drives in a RAIDZ2, you end up with 10.9TB - 2.18TB = ~8.72TB of usable space (80% rule).
Now to throw one more thing at you... by default LZ4 compression is turned on. This means that if you have any files which can be compresed, you will be able to store more data. This is done behind the scenes so it's a benefit. If the file is a video or zip file, those likely cannot be compressed so the file is just stored. Keep this in mind as well, at times it feel like a Christmas gift when you examine your data.