To answer your first bullet:
I have no experience with this specific controller so you may need to check the documentation to confirm anything. If Windows has the right driver in for the controller, rather than just seeing it just as some generic SATA controller, then you should if the BIOS supports it be able to make a RAID1 array using the existing data as the template. If you don't have the right config in Windows then you may have trouble as enabling the RAID functions is likely to change how the controller is seen by Windows. I strongly recommend taking a full backup before trying this, in case the RAID controller creates the new array and blanks it rather than taking the first drive as the initial template.
Under Linux's software RAID this is usually done by creating a RAID1 array in a degraded state with just the existing drive, adding the new drive in an error (unsynchronised) state, then forcing a resync to bring the new drive to where it should be. Your RAID controller might offer a more intuitive method than this, but might not support the process at all. IIRC it is possible to convert an existing single drive to RAID1 with Windows' software RAID, even if it is the system volume, but I'll leave that to a Windows expert to take up as I'm not overly familiar with that aspect.
To answer your second bullet:
If you use the motherboard's RAID controller then you can pretty much guarantee that moving the drives to another motherboard will result in the RAID array not being usable, unless the new motherboard has the same chipset.
To get around this either go with a good hardware RAID solution (so you can move the RAID card with the drives or have more chance of purchasing another, compatible, one later) or use software RAID (I don't know about Windows, but Linux software RAID migrates between machines quite nicely). If you need compatibility between multiple OSs (so, say, both Windows and Linux can access a filesystem on the same RAID array), then of those two options good hardware RAID it will have to be.