So what's the point of the secret-key then?
Sounds like you guys just discovered that you should have been storing the secret-key as a salted hash instead of cleartext. But instead of simply fixing that, you bolted on a whole new secondary password system that makes the original one redundant.
This does not instill confidence.
The secret key is used to check your message signature and as such we must use it to calculate the signature and check it for validity. The signature ensures that your message was not tampered with by a MITM.
If you would like any clarification about the relevance of the fields please contact
support@bitfloor.com and I will be happy to go over the details. It will help me in understanding how the documentation can be clarified.