From my own experience, yes, you have to put down the whole thing piece by piece to look nice; no workaround i know of when using the vanilla sets (Ex: grasslands_structures.png). The "grasslands.png" you linked is mostly outdated, thats why it has the rotten tower. You should have a look into the art repository, tiled folder to see what recent modders used.

1) You can just import any .png you want and give it a full size or cut it into needed chunks. Tiled will ask you the model size while importing; so if its a .png of a house of 200x200 pixels, you input 200x200 and it creates a single "chunk", if its a file 1000x800, with multiples houses, each measuring 200x400; you input 200x400 and tiled will auto-cut those chunks into each house whole. Sounds weirds but its like that...

2)Not that i know of, i place them manually.

Im attaching an example of what i explained.

One more thing, adding more models than vainilla sets have, has a problem, you will need to create a new tileset definition so the models are shown ingame.

That is done with a phyton script "tilesetdef-generator" included somewhere in the repository; to keep things sane i just use extra buildings into city hubs and use vanilla sets for combat maps. That way i just have a handfull of "custom" maps with the need of a custom tileset definition. (oh, i almost forgot, you need to install python 2.7 for it to run)

The tileset creator instruction is like this:

PS C:\Users\danim\Desktop\flare-engine_v1.11-68-gd1a5e854\mods\HERESY\tiled\grassland> py tilesetdef-generator.py Act1Triston.tmx

I use it from windows powershell, capitals+rigth click over folder, so i dont have to add any directions, the script need to be inside the folder with the map, replace map name and done.

After that you have to put the created file into the folder "/tilesetdefs" of your mod (create it if you dont have it) and replace the set the map uses to your own:

tileset=tilesetdefs/tileset_grassland.txt > tileset=tilesetdefs/tileset_triston.txt (inside the map file saved into flare format)

Im telling you, Flare is not for faint hearted people, you should check all the questions in the forum where i stumbled into this knowledge.

I almost forgot, there is a workaround to all these, you can make those new buildings as npcs. You have to declare them somewhere else (.txt files) and set up the collision map by eye, but its less painful if you just want to add a single building.

But as you can see, i added that whole cathedral and house as singles, uncut.

@Danimal A few corrections:

1. You'd have to create the stamps yourself, but you can use Tiled's "tile stamp" feature for placing commonly used groups of tiles. For example, I use this on the 16 grassland tileset floor tiles to make a 4x4 square (the texture repeats cleanly when laid out like this).
2. I highly recommend not using tilesetdef-generator anymore. Instead, use the Tiled extension from flare-tiled-tools. It works better in general and even supports external tilesets in addition to embedded tilesets. Once installed, using it is as simple as going to File -> Export and then selecting "Flare tileset definition" as the file type.

Thanks dorkster, ill try for the next custom map;