i can help you abit, but not too much
Priorities: as far as i've gathered, they determin the priority of tiles overlappting eachother and the player, 5 means they will overlap everything and float on the very top, like pipes in the celling wile 0 means that everyting is ontop of it, also the positions of the tiles in the layers matter aswell, if you have a tile on the 2nd player with a piroity of 5 while you have a tile on the top layer with a piroity of 0, the 5 will show up on top, i get that when i stick fences behind a house under the roof
Passages: i'm not sure what you mean by this but i saw your talking about here you have 4 arrows and you can chnage then to dots, this shows the direction the events an player are blocked at on that tile, if you have a tile with north as a square while the others are arrows, it means on that tile you can't leave it by going north or enter it by going south, it's like the passibility with the X, O and [] but more control on where their blocked, you would mostly use this all the time for cliffs where you can walk to the edge of one, go around and to the other side of it giving the impression that you've gotten high up or went down
fixing up walking on trees, well if you look on the defult RTP Tilesets in the database you can see just how they set up a tree perfectly, follow that example and you should be fine
that's all the help i can give