My presbyopia issues did make this very difficult for me to do with out the traditional box.
Unassisted, I was able to get the cat into focus. Wow, he is really long, once 3d comes into play. I had to resize images for my display screen. The distance between the centers of the images have to match the distance between your pupils, or be even slightly less.
But I had real trouble getting the tool into focus. Finally I edited in a red line over a selected point on both images, then I put my face very close to it, and triied to imagine looking at a distant ship or sunset. Once the image locked, where three images appear, I could slowly sit back until sharper focus came back.
Once locked, the middle image has 3d, and the other two will be out of center and only 2d. The old boxes elimiate the images at the side, plus they use lenses make the close focus seem more distant, which all helps.
For the rest of us... The easiest way without a box; After resizing just under 2.5inches (63mm) between centers, put a sheet of cardboard (or envelope) on edge between the images on the display surface, and then put your nose against the edge closest to you. Then look to the imaginary distance, and try and relax your eyes. It should snap into place. With practice, you can ease back, until your sharper focus is restored. You can even drop the cardboard at that point.