Consider a particle moving through a potential of the form $$V(x)=\begin{cases} 0 & x<0\\ V & 0\leq x < L\\ 0 & x\geq L \end{cases}.$$ We may write out a solution to the time-independent Schrodinger equation for each of these regions $$\psi(x)=Ae^{ikx} + Be^{-ikx} \quad k\hbar = \sqrt{2mE} \quad \quad \text{Region 1}$$ $$\psi(x)=A'e^{ikx} + B'e^{-ikx} \quad k\hbar = \sqrt{2m(E-V)} \quad \quad \text{Region 2}$$ $$\psi(x)=A''e^{ikx} + B''e^{-ikx} \quad k\hbar = \sqrt{2mE} \quad \quad \text{Region 3}$$ and use the fact that the wave function and its first derivative must be continuous at $x=0,L$ along with the normalization requirement to find the coefficients for the exponential terms in the wavefunction. So far, this all makes sense.
However, when we consider the transmission probability $T$ of moving through the barrier, it is defined as $$T = \frac{|A''|^2}{|A|^2}.$$ The justification for this is that this is the ratio of the flux density ($|A''|^2$) of particles moving away form the wall in Region 3 to that of the particles moving toward the wall in Region 1 (which is proportional to |A|^2). This is the part that is confusing to me. The wavefunctions for Regions 1, 2, and 3 all are parts of a single wavefunction representing the stationary state of a molecule in this system. This seems distinct from saying: prepare a particle moving to the right in region 1 and then measure the flux being transmitted through the wall. Perhaps I am understanding the idea of flux density incorrectly. I apologize if my question is poorly phrased, but I was hoping someone could clarify how to correctly think about flux density and $T$ in this case.