You have probably figured it out. Go to fusion menu, on the left pane there is a small alignment control panel. I would try leaving everything at default first and click on the alignment button, then the cursor becomes a magnet icon having a subscript "A," click on one of the scan results on the right column, then click on the other when the cursor has a "B" subscript.
Projector: Acer K132 + 1/2/4/10 X closeup dai. 52 mm.
Camera: Grasshopper 3 GS3-U3-28S4C-C (@ 1600 X 1200, 30 fps); Lens: 8-50 mm F/1.4.
Computer: USB 3.0, CPU: 2.6-3.5 GHz, GPU: 3G NVidia 970M, 32G RAM.