You can choose what is transferred. I have used it several times in the past and found the whole process fairly painless. In your scenario, once you have set up your new PC, I would transfer "My Documents" "My Music" etc. I would only transfer "Settings" from the old PC if there is something very specific and detailed to set up on the new PC that you are currently using on the old PC.
Surface Pro 4 UK release date, price and specs: Thinner, lighter, faster with new Type Cover and Pen