I've found that vertically placed guides are the best way to do a vertical interlock like this one.
Take the bottom box you want to interlock, and push a guide up against the side of it so that some of the guide is higher than the top of the box like this:
Then do the same thing on another side of the box, but not the opposite side, so you have two guides forming a corner, like this:
Then place the top box you want to interlock on top (I used a single box here), pushing it into the corner formed by the two guides, like this:
Then set the bottom box not to spawn and start a new round so that the top box is floating like this:
Then pick up the single box and move it lower down, but still pushed into the corner made by the guides. Get it to the height you want it, save the game, then quit:
When you spawn the first box back in, the top one should be interlocked smoothly:
Hope this helps.