Hey, I think I can help.
For your first question, the first thing you need to learn is there are Priority options for each physical tile you place on the map. Observe:
The red box in the image highlights the Priority options. These options make Mario or any NPC that stands over the tile act as Priority 3.
Priority 3, or P3 abbreviated, works like this in layers of a cake:
P3 <- The layer on topmost
P2 <- The layer on second-most
P1 <- The layer on bottom-most
If you look at the cake from the top, you only see the topmost layer. Same with this.
Any tile can have P3 set to them on the main tiles, but the solidity tile will actually override that, making any sprite/NPC that stands over it, P3.
For the second question, if you have no layer 3 tiles, set the Layer Priorities on the left-hand box to 0
. It's under the LAYERS tab.