Noem, one thing isn't clear, do you have two or three disks?
If you have three then there is no need for any convoluted messing about, and most likely data loss. Just put two disks in the NAS, format them as RAID1 then transfer the data from the third disk.
If you only have two disks, the first thing you should try and do is to transfer everything from your NTFS formatted disk to your computer. Having done that, you can put two drives in the NAS and proceed as normal.
Trying to format one drive at a time will, I think, just give you a JBOD setup, not the RAID1 that you want. You may be able to convert JABOD to RAID1 but there is the risk of loosing everything.