Sorry, but I don't understand your question about your software.
However, as far as CTR completion is concerned, Form 112 expects you to provide identification for an entity just as you do an individual. Assuming the entity is the person on whose behalf the transaction and is conducted is your customer, then your bank should have identified it at account inception. All they need on the CTR is a recitation of what documentation you used to do that.
If you are relying on your software to populate the appropriate field on the CTR, "Unknown" won't get it done.
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In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.