Problem solved, all it took was my Portuguese ingenuity or "Desenrascanço". The uncanny ability passed down through the generations to solve any problem with merely a penny and a string. ( I didn't solve the problem with a penny and a string but you get the point ).
So here is the solution:
- Connect one of the disks to the motherboard, let's call source from now on.
- Install Ubuntu Server on source disk.
- Run sudo apt-get update
- Run sudo apt-get upgrade
- Install dmraid, by running sudo apt-get install dmraid
- Put the modules dm-mod and dm-mirror inside the /etc/modules file, just sudo nano /etc/modules
- Connect the source disk to the PCI card on the first SATA port, connect the other disk on any other port
- Create the RAID 1 array. And boot the computer using the RAID array, it's going to boot, because one of the disks is bootable.
- Confirm that the raid is running by issuing: sudo dmraid -ay, something on the lines of this should appear: "*sil_bhbgdjddagcc: 0 976771072 mirror core 2 131072 nosync 2 /dev/sdd 0 /dev/sde 0 1 handle_errors.*"
- Disconnect the second disk ( the one that is not the source disk ).
- Boot from the array again, and make a change to any file. Then shutdown.
- Connect the disconnected drive and rebuild the array.
- Wait a long time...
...and if everything went well you should now have a running RAID 1 array on your server.
How did I check if the RAID 1 array was working? Just boot from each drive separately connected to the motherboard, if it boot's then it means that the rebuild was done correctly.
After checking that the rebuild was done correctly you have to rebuild again. After finishing with this boot's and rebuilds, you just have to change one file on one disk while using the RAID 1 array, then shutdown, disconnect the disks from the array.
Then boot from them separately and check for the change you made to that file is on both disks, if the changes are there, it means the RAID 1 array is working. Then it's time for another rebuild, and the system is ready to use.
Why do I have to rebuild the array every time I boot from one or another, because every time the server boots there are changes on the disks, that's why.
This solution doesn't work with another types of RAID arrays, RAID 5 should be a no go, because the data is spread across the disks, RAID 10, shouldn't work either because the data is stripped and mirrored, RAID 0 is not a problem because it's detected by the install.
Best Answer
When asked: Active MDADM containers (Intel/DDF RAID), choose "yes"
It will then ask: Activate Serial ATA RAID device, at this point wait and switch to a shell by pressing "alt+f2"
Press Enter to activate the console
Then run the command "mdadm --stop /dev/md127"
Next activate the intel dmraid by running the command "dmraid -ay"
Press "alt+f1" to go back to the installer.
Now you can answer the Activate Serial ATA RAID device with "No".
It should now pick up your Intel RAID.