I wan't to put all faces and parts of block in one texture instead of putting them in separate files limited by 16x16 resolution. How can use sprite set for block that contains all textures of block? I tried to put all textures of block in one file, it threw warning that says that I broke aspect ratio of resource.

 

Textures are not limited to 16x16, that's just the default aesthetic of Minecraft.

It is recommended that you keep your textures square/rectangular and separate. And let Minecraft stitch them all together.

However if you MUST use a pre-combined texture. You just need to set your UV's in your model file correctly. Such as Instead of using 0, and 1. Use 0 and 0.333333 if it's a 3 column texture.