I've heard the total energy is zero, but I've also heard it cannot be said to be zero since there's so much unknown stuff in the universe. Is that true?
Conservation of energy doesn't actually apply in any straightforward way to cosmology. The modern understanding of energy conservation is that it is a consequence of Noether's theorem and time translation invariance. In other words, the laws of physics are the same as they were yesterday and they will be tomorrow. This gives rise to the conservation of energy. When the expansion of the universe is important you are doing physics on an expanding background. This breaks the time translation invariance and hence the conservation of energy.
It can be argued that the gravitational field has energy and when this energy is included you get zero total energy for the universe. The problem with this is that there isn't an unambiguous definition for the gravitational energy of an expanding universe (this is somewhat controversial).
I think it can be safely stated that no one really knows the answer to this, because like you've said, there's so much unknown stuff in the Universe. There's that dark matter and dark energy stuff that's pretty mysterious as of today.
Here's a Wikipedia article on the zero-energy-universe, btw.
I think it would make sense for the total energy to be zero. Because, really, if its not, then how can that be? Where did the energy come from? Its pretty safe to say that the conservation of Energy is something that's widely accepted and held to a pretty high degree. The reason why it would be zero is because all of the positive energy equals the amount of negative energy the Universe has.
I hope someone else can answer this better than I can.