I smoke in order to get their heads down, then lower the upper box with a 15-degree (or thereabouts) offset so that the first meeting of sidewalls has a relatively small contact area. Then, the upper box is rotated until it lines-up with the lower box.
It's not a perfect method by any means - as sometimes a bee will make a dash for the closing gap - but it works well most of the time. With a bit of practice, it becomes easy enough to combine the lowering and rotating into one smooth action, when there's much less chance of shearing a bee in two.
To ensure that the boxes are lined-up (although I've never really thought much about how I do this before) - all I do is place my thumb and forefinger of each hand across opposite corners of the boxes where they both meet. If line-up feels about right, and looks about right - then I just carry on ...
When, over the years you've seen broken boxes, rotten boxes, hives tipped over and so forth - whether boxes are lined-up absolutely perfectly seems to be not all that important in comparison. I do have my own obsessions, though - but that ain't one of them.
LJ