I'm finding that adding a desktop icon through the main menu, as you describe, that KDE will happily place the new icon in the upper left of the desktop on top of the one already there... and it will keep stacking them on top of one another if you add more.
Not only that but if you add icons this way they won't align to grid even if you check it off to do so. The way I found to align to grid is adding app icons through a right click on desktop and Create New... Link to Application.
I'm not really familiar with plasma/plasmoids as I've only upgrade a couple of weeks ago so I may be missing something everyone already knows. Hope this helps.