The short version first:

• Status of your current setup Yuppers, if you would switch from your current RAID setup to Software RAID, you would have to delete the RAID set in the controller-BIOS (results in complete data loss)
• MDK tools for RAID setup I don't know what RAID setup utilites come with MDK these days, but you can take it as granted that the kernel comes with SW-RAID support. As it goes for the relation between drives/partitions, logical volumes and all that ... (lean back, relax, this is going to be lengthy

What you have found on the MDK forum is about what I was talking about in my first post ("LVM"/"Software RAID").
In fact, "onboard hardware RAID" - as postulated by the motherboard manufacturers - is in no way a hardware solution. It's a marketing buzz-word, and indeed: you'd probably be better off with a genuine linux software-RAID solution.
The linux SW-RAID-technique is what you might know from Windows as "Dynamic Volumes". Compared to the heapo-onboard solutions SW-RAID has some major advantages. The most interesting one is that you can use partitions for your RAID-volumes instead of whole drives. Time for some rotten ASCII-art, I say :)

Check a detailed explanation here