In this reference just in the beginning the author gives the theorem (Theorem 1) of the conservation of a Hamiltonian flow $\phi_t$. According to it this means that $$ \frac{d}{dt}\phi_t^* H = 0$$
I am confused on what the $\phi_t^*$ is and how it acts on the Hamiltonian function $H$ (let's assume it is a potential in classical mechanics). Additionally I would like to ask what is a "level set" of $H$.
The Hamiltonian vector field defines a flow on a symplectic manifold, called a symplectomorphism. A diffeomorphism $f: (M,\omega) \rightarrow (M',\omega')$ between two symplectic manifolds defines a symplectomorphism where $f^*\omega'=\omega$. The $f^*$ is the pullback of $f$.
Assuming that the Hamiltonian function H is not constant on any open set we simply need to plot the level curves giving the solutions of the system. These solutions will live on these level sets.