Press F7 to have chunk grid shown. Every red square is called chunk. In every chunk can only 4 different textures be used. By using ctrl+left click witht your 3d paint tool you can get list of textures which are already used on chunk.
To paint with texture for which you lack space you have to get that space. You can either erase all texturation from chunk by using ctrl+alt+shift+left click, or you can use Texture swapper (its included in 3d paint tool and can be accesed in top right corner of application while that tool is selected) to swap some unused texture for a new texture.
EDIT: Btw, such things are surely described in tutorials, I would suggest you to read them and to read them whole. It saves a lot of both your and our time in the end
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