Assuming the 6v are two separate banks and not just a single bank separated physically but electrically one...
No, it does not make sense to have 3 banks. Two banks makes sense because if house loads run down the house bank, you can use the starting bank to start the engine (or generator) to get the house bank recharged (may not be the ideal charging scenario but at least you aren't dead in the water).
For the same total amp-hr rating, a single large bank will actually have higher amp-hr available due to the peurket effect. It will also be able to absorb more amperage when charging, so you can put amp-hr back in faster.
A third bank only adds complications with no real advantage.