I keep on hearing that behind all matter is just waves of energy. I even hear that it is made up of small energy tornado-like waves. This is theoretical physics right? If so, how strong is the theory.
Energy isn't really a substance, it's a property of things. Matter can have energy; fields can have energy. In quantum field theory, fields are the fundamental unit, and particles are represented as excitations of fields. Basically, you can think of the field as some function that takes on different values (sometimes zero, sometimes not) throughout all space, and the particle is a localized vibration of the field.
So possibly you're hearing a muddled version of this, that everything is really fields. Also, in quantum mechanics a particle isn't really like a classical particle, but rather is something that has wave-like properties and particle-like properties -- this is known as the wave particle duality. So possibly you're hearing that everything is really waves, and it is, but it's particles as well.
As far as "How strong is the theory?", if you mean how well tested, then it's not an exaggeration to say that it's probably the most well tested theory humans have ever invented, at least in terms of the degree of precision with which it's been tested. The predictions of quantum electrodynamics, which is based in quantum field theory, have been verified to ten parts in a billion. http://en.wikipedia.org/wiki/Precision_tests_of_QED