Do you want to click on some position in the layout and draw the tile on the tilemap? Can you provide a c3p? Because, as far as I know, there is no problem with this in C3 and you can use several tilemaps in the same layout, there are no technical limit. Most likely you are using wrong coordinate.
Tilemaps have a size limite of 1px, but It's not recomended to use tilemap like that. It would have a bad performance since It was design to draw bigger tiles like 16px or more and avoid repetition using sprites. If you create a tilemap of really small tiles, the performance would be the same or worse if you were using sprites. Imagine how many sprites/tiles would you need to draw the whole screen.