Ok, I know that! I am one of the main developers of Encog. :)
We have improved support for this in Encog 2.4 (which is in beta), however even the current version supports this. In Encog 2.3, the offset is called a threshold. Therefore, create your layers by indicating that you WANT threshold values. This basically creates bias inputs for each of the levels you specify having threshold values. I build it all in one layer, because it improves productivity, everything works the same way.
We really discussed this, and we clarify it in Encog 2.4. You can read the discussion here.
http://www.heatonresearch.com/node/1477
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