The only thing that matters in the save/load menu is the save slots you created via the floppy disk tool, the regular object areas you created don't matter & are only used to indicate which save slot the player has selected & also to execute the save slot, however let's say that the player then accidentally clicks on another slot when they go to press the save/confirmation button - the thing is that those save slots are layered on top of everything, which is why you can't generate a confirmation button above the save slots themselves.
Well you can store the selected slot number in a variable and feed that number back when executing the save or load when hitting the confirmation button. But that requires scripting.
(system.selectedSavegame - luadocs says "readonly" but you can actually assign a value, too)
And that might answer you question @nicolaj, how the engine knows what slot is selected. The slots (created with the floppy disk symbol) are numbered internally (in the sequence they were created, I guess). When clicking on a slot, the number is stored in systems.selectedSavegame, and on that slot the action is executed.
