positioning with different heights

Solution 1:

You can control which floor you're going to using the mouse wheel.

Alien ships, however, do have the annoying tendency to have strange architecture which confuses the floor-selection mechanism. My work-around is to play with both the mouse-wheel to control the floor and q and e to control the angle, until I get my cursor in a location where there's nothing behind it, so it has to choose the upper floor.

The same can be done with the dpad on consoles or on a gamepad for windows.

Solution 2:

It appears that on some maps, the "what level the cursor wants to stick to" and the "what level is being drawn" are off by one, as mentioned in the other answer. e.g. the movement cursor is sticking to level 2 but the game is drawing level 3 (the roof).

There are two methods to get around this in these cases:

Say you have a soldier that you are trying to place onto a tile at level 2:

1 - put the "cursor level" too low, at level 1, so that the "visibility level" is correct, at level 2, and then rotate the map with Q and E such that no tiles at level 1 are lined up behind the tile on level 2 you wish to move to. With no level 1 tile to prioritize, the cursor will stick to level 2. I have never encountered (so far) a map where I was unable to find an appropriate angle, but it is a pain.

2 - put the "cursor level" correctly, at level 2, so that the "visibility level" is too high, at level 3 (the roof), and the blindly click through the roof. On some maps, this is actually easier than the first option. You can put the cursor level at 1, where you can see level 2, place the mouse over the tile you wish to move to eventually, go up a level with the scroll wheel, which will make the cursor stick to the correct level but draw the roof on top, and just eyeball-double-check that the 3-D cursor box outline appears where you think it should, and click.

Solution 3:

It's a question of which height-level is currently selected, if your target box jumps down the edges of platform it means that you selected the lower level (which you probably did because the roof of the UFO was in the way and you couldn't see your soldier).

I have not tried it yet, but on PC you can also zoom in and out (forgot the hotkeys now, zoom out was 'g' I think), so you can both see your soldiers and still have the appropriate level selected. (as mentioned before, rotation with 'q' and 'e' also can help you see your soldier)

Otherwise you can always maneuver semi-blindly (you still see the outline of your other soldiers on that level).