The poem Bhaja Govindam indicates that there was something that Sankaracharya realised which is beyond the advaita that meant non-duality and refers only to union of the Self/Atman with Brahman the universe. This philosophy does not have any sound basis for acquisition of knowledge about the universe because God has created Brahman and hides within Brahman through a process of self-transformation in which He is Brahman yet separated from it. The philosophy of this advaita governed by the deity Brahma. Perhaps Sankaracharya thought that Brahman generated Govinda as Ishwar.
The only viable path to the knowledge of ultimate reality is through bhakti (devotion) that God exists and then go in search of Him to try and prove that this is true. It is done through the process of satya-advaita or oneness with truth, that is to say truth-accommodation. For it to work one must give up all attachments and try and expose truth and adopt the new truth realised. In other words discovering reality from practical experience and knowledge through science as far as it will take us and then from conjectures one by one examining all questions and rejecting that which makes no sense. Truth is the highest discipline (refer to Mundaka Upanishads Satymev jayate). Discovering the truth about the existence of God cannot be done by contemplation and meditation but through a process of submitting oneself to God and to let him take the reigns of ones mind. If God is moved enough to listen to the sadhaka, he will plant thoughts into the mind of the person that will be revelations to make the person realise God. He may also give the sadhaka visions and other experiences for realisation to be completed. The ultimate truth to be realised is achintya bheda abheda tatwa in which a person realises that God is distinct from the jiva but simultaneously he lives the life of the jiva. The yogi can and indeed must use easily available techniques of investigation to try and realise the difference. It is not easy and can take a dozen of more years before there is irreversible realisation. This alone will show the jiva when he can be absolutely sure that a thought he has had comes with the approval of God and so should be put into action. One lives life according to this guidance without fail for the process to continue to be reinforced. Without the use of techniques that will confirm to the person if he is having a genuine darshan of God there is no way of telling whether a thought is self-generated or given by God. I have described this process earlier: https://satyaadvaita.wordpress.com/2014/06/08/advaita-and-satya-advaita-in-brahmanism/.
I am basing this on my own realisation which I find is consistent with the following report of an intricate relationship between the jiva and Sri Krishna by the founder of the idea, Chaitanya Mahaprabhu, back in the 15th Century: http://en.wikipedia.org/wiki/Achintya_Bheda_Abheda. ‘Achintya bheda abheda ‘ translates as inconceivable ‘difference’, and ‘non-difference’ there is oneness and separateness simultaneously. The difference and non-difference that I noted is when one has thoughts for action as the person (jiva) and when the thoughts for action are from God through the jiva. There is a way to determine God’s wishes and advice if God chooses to respond to the devotee.
The practice of achintya bhed abheda tattwa in the manner described here stretches Vedanta in attempting to realize what is in existence before and over and within Brahman which is to say the Creator of Brahman. That something is Supreme God. I have shown that it is possible to have a one to one relationship with this God too but only when He chooses to. No mantras exist to invoke this God. He only manifests himself from yuga to yuga at times of His own choosing. This Creator God is Sri Krishna, the imparter of the wisdom of sanatan dharma to humans. Acinta bheda abheda tatwa is the experience of union with this God. This is not a new theory as Chaitanya Mahaprabhu is associated with its original discovery. However, it should be noted that a relationship with God through advaita is not available to everyone so that this term of advaitic representation is not the general condition. God does not run every individual’s life. He only guides the devotee who genuinely in his or her heart is seeking pure and pristine truth keeping all options open through what I have described as satya-advaita.
It is highly unlikely that Sankaracharya had undertaken any studies that might have revealed to him that Sri Krishna as God was both external and internal to the Universe and that Brahman comprised of physical energy and consciousness. Sri Chaitanya was the first person to describe achintya bhed abheda tattwa that I confirm as a genuine mechanism available to God.