The tile set (or tile library) is nothing more than all used tiles after another. Yes, this looks like a mess but that’s how a tile library works. You can move tiles in the tile library if you need a certain order but this is not always required.
And tile mapping means: Have a set of unique tiles. Have maps that refer to those tiles. A tile map entry is just like a pixel that uses a certain palette entry (0,1,5,23…). A certain map entry uses a certain tile (0,3,8,88…).
The advantage of this tile mapping is mainly the small amount of memory you need and the automatic reuse of objects, mirroring etc. .
You can export such tile maps (along with the tile library) to use it in a game engine that can do tile mapping, e.g. Construct from https://www.scirra.com/ . Or you can use Tiled http://www.mapeditor.org/ to create level maps while you use PM to rework the tile set.
The tile library is not there to have a bitmap that defines objects (visually correctly placed) made up of a couple of tiles. It’s just the list of the single tiles, no more, no less and the tile map refers to it with the tiles placed there.
It is not meant to be an object library, although it can make sense to select a single tile from there and place it down. It also makes sense to have tiles close to each other there that belong together, but that’s not important.
But if you want objects then use a tile map/frame and place the tiles and tile groups there and pick them up from there. You can either use a second frame of the current project or you can go to the tile mapping settings and add a dependent project.
A dependent project is a second project that shares the same tile library. Each frame of a layer is again a tile map and you can place your objects there. You can arrange them on different layers and give the layer a descriptive name like “plants”, “rocks”, “items” whatsoever.
Whenever you need an object, go there, pick it up and use it in your main project that defines the level map (or a couple of).
This way you can also create tile animations. Just create a dependent project that uses the tile map size according to the object you want to animate, no matter if it’s single tile sized or uses 2x2 tiles. Just add as much frames to the project as you need for the animation and then start drawing your animation.
It will create the tiles accordingly. You can then shift them around in the tile library if you want to have the different tiles forming an animation side by side.
Please also have a look at the tile mapping primer: https://www.cosmigo.com/promotion/docs/onlinehelp/tileMappingPrimer.htm
and here as well: Tile library: user-defined width, multiple selection
I’m currently optimizing a lot concerning the tile mapping system to make things work more smooth, but this mostly concerns tile placement and drawing, not the tile library (in general). See here for some sample: https://twitter.com/CosmigoPM/status/932251260174127105
The tile library is, as described, a technical element when working with tile maps. I only optimize some drag/drop handling and multi selection there.
Hope this helps a bit. It would be great if you described in more detail what you are doing. This helps me to better understand and to, maybe, give better advice and maybe add certain functions.
After the latest tile mapping engine changes some tutorial videos will be created that show the things I was talking about.