I'm having this problem for a while, but I'm still failing to realize what is bothering me in this, so here is my attempt at explaining my doubt:
I have the time-independent Schrodinger equation: $$-\frac{\hbar^2}{2m}\frac{\partial^2}{\partial x^2}u(x)+V(x)u(x)=Eu(x).$$ If, for example, I want to find solutions for $E<0$, in an infinite well $V(x)=0$, I have: $$\frac{\partial^2}{\partial x^2}u(x)-k^2u(x)=0$$ and specify $k^2=\frac{2m}{\hbar^2}|E|$.
But now consider the potential barrier, with $E<V_0$, $$V(x)= \begin{cases} 0, \hspace{0.5cm} x<-a\\ V_0, \hspace{0.5cm} -a<x<a\\ 0, \hspace{0.5cm} x>a \end{cases}$$
And therefore I would know define $\alpha^2=\frac{2m|E-V_0|}{\hbar^2}$ and $$\frac{\partial^2}{\partial x^2}u(x)-\alpha^2u(x)=0.$$
Do these parameters $k,\alpha, etc...$, have any special conditions? Must they be always positive? For example, Gasiorowicz, 3rd edition, page.71, specifies, for the potential barrier, $\alpha^2=-\frac{2m(E-V_0)}{\hbar^2}$ and writes: $$\frac{\partial^2}{\partial x^2}u(x)-\alpha^2u(x)=0,$$ but now that would be $$\frac{\partial^2}{\partial x^2}u(x)-(-\frac{2m(E-V_0)}{\hbar^2})u(x)=0\rightarrow\frac{\partial^2}{\partial x^2}u(x)+\frac{2m(E-V_0)}{\hbar^2}u(x)=0.$$ Why not only $$\frac{\partial^2}{\partial x^2}u(x)-\frac{2m(E-V_0)}{\hbar^2}2u(x)=0,$$ instead?
I'm sorry if I was unclear!