I have spent several days trying to get a good result, this has worked for me. Try it and see if it works for you too.
You will need a laser pen. I have one because I have cats...:) I put it in a Cameo pen holder! The dot is actually very small but hard to photograph! It has to be one with a centre point, obviously.
Put your designer paper onto the cutting mat and in SCAL, make a rectangle that is at least half an inch smaller all round than your scanner can cope with. IE if you have an A4 scanner, you want to cut a rectangle that is smaller than that.
On the corners, use a marker pen to really darken them, like this.
Scan the paper. I find that for me, PNG saves as the actual size, while JPEGs will be huge images, bigger than the mat!
Trace the scanned image in SCAL, adjusting if needed, making sure to capture the corners. This is important to make sure the whole image can be lined up. For some images you may want or need to do a manual trace.
In the position menu box, put in whole numbers to move the image to make the bottom right corner align with a square on the mat. It does not really matter which one, but it does make sure it is obvious if you have accidentally rotated or skewed the image.
Set the paper into a corner of your mat as in the image.
Put a laser pen into the blade holder grip. Make sure it is vertical because if not the spot will not be in the right place. I use a bit of tape to hold the button down.
Line up the laser just inside the bottom right corner of the paper. I really do mean JUST inside. Putting it actually on the cross lines, the cut will be off - or at least that is what I found. I find it easiest to have the grip levers in the up position, then put them down one at a time when I have the mat positioned.
Set the origin when the laser is lined up. Now you can do the cut, make sure you select 'Origin' in the cut setting box.
The good thing is that once you know that origin is correct, as long as you don't switch the machine off or take the mat out completely, you can use the same method to cut more printed papers, just by lining the bottom right corner to the correct square on the mat after you have done your trace.