You have some space $\mathcal{M}$ (e.g. $\mathbb{R}^3$), you have time which are values in $\mathbb{R}$, you have a particle characterized in terms of coordinates $\{q_{\ i}(t)\}$ for it, which is a map from time into space. Lastly, the theory is essentially given by a mathematical relation
$$D(\{q_{\ i}(t)\})=0,$$
which gives the dynamics. For example
$$D(\{q_{\ i}(t)\})=\vec\nabla\Phi(\vec q(t))-m\vec q''(t).$$
Noethers theorem is a mathematical insight on specific such dynamical systems which gives an energy function $H_D$, such that
$$\forall t:D(\{q_{\ i}(t)\})=0\ \ \Longrightarrow\ \ \forall t:H_D(\{q_{\ i}(t)\})=E,$$
where $E$ is some real depending on the initial conditions.
For the above example, you have
$$H_D(\{q_{\ i}(t)\})=\frac{m}{2} (\vec q''(t))^2+\Phi(\vec q(t))=E.$$
The Hamiltonian gives the total energy and as its value here is seperated in the two summands $\frac{m}{2} (\vec q''(t))^2$ and $\Phi(\vec q(t))$, the energy-distribution can vary between the two. One can speak of "storing" the energy in the kinetic or the potential energy part. At the same time, the value of $H_D$, and also of $\Phi$ alone, critically depends on the value of $\{q_{\ i}(t)\}$ and so it makes sense to talk of the particles potential energy, i.e. the potential energy associated with the particle. In conclusion, the dynamics determines the energy function and the value of all energy expression necessarily depend on the functions $(\{q_{\ i}(t)\})$ (together with its derivatives). As $H_D=E$ is the actual unchanging energy of the particle, you can speak of some energy being stored in the potential in the above sense, but only if you're aware of the fact that this only makes sense in the context of a particle given by $(\{q_{\ i}(t)\})$ which fulfills the dynamics of the system.
As a side note, what is said above essentially also translates to field theory. I.e. things work out similarly, if instead of particle coordinates $q_{\ i}(t)$, you speak of some fields $\psi_i(\vec x,t)$ and dynamics
$D(\{\psi_{\ i}(\vec x,t)\})=0$, like
$$D(\psi(\vec x,t))=(\Box+m^2)\psi(\vec x,t),$$
in the case of the Klein-Gordon equation. In (quantum) field theory, it is actually more common to directly express the dynamics in terms of a Lagrangian or Hamiltonian.
Now if you have a theory with more dynamical objects than a particle (for example if you consider interactions between charged particles together with a changing electrical field), then the total conserved energy function will depend on both of them. If, in this case, you still make sense of associating two energy quantities with both objects (like if you can make out term which only depend on one of the field), then it's suggestive to speak of energy exchange between the two. In that case "energy stored in the other field" is a an intuitive notion. To keep track of thing, you want to make yourself clear what the quantity is, which is actually conserved.