First off I found this video that shows stacking in action. You can place items based on other items, but then the first can be removed. doing this repeatedly allows you to suspend objects in mid air. This is how many people use various counters pieces to make wooden walls, seuspended walkways, multilevel areas and more.
Here is a good example of multi-level base design --- from the Justice Server, Heirs of Talos. According to the forums they spent over 20 million prestige on this base...