Para cortar ecuaciones largas debemos utilizar el entorno \begin{eqnarray}............\end{eqnarray}
y utilizar doble slash (\\) donde nos interese cortar la ecuación. Para que los trozos de la ecuación no se numeren debe emplearse \nonumber.
\begin{eqnarray}
W=\underbrace{\left\langle\phi(1)\left|-\frac{1}{2}\nabla_1^2\right|\phi(1)\right\rangle}_{\zeta^2/2} \underbrace{\left\langle \phi(2)|\phi(2)\right\rangle}_{1} + \nonumber\\
\underbrace{\left\langle\phi(2)\left|-\frac{1}{2}\nabla_2^2\right|\phi(2)\right\rangle}_{\zeta^2/2} \underbrace{\left\langle \phi(1)|\phi(1)\right\rangle}_{1} + \nonumber\\
\underbrace{\left\langle\phi(1)\left|-\frac{-Z}{r_1}\right|\phi(1)\right\rangle}_{-Z\zeta} \underbrace{\left\langle \phi(2)|\phi(2)\right\rangle}_{1} + \nonumber\\
\underbrace{\left\langle\phi(2)\left|-\frac{-Z}{r_2}\right|\phi(2)\right\rangle}_{-Z\zeta} \underbrace{\left\langle \phi(1)|\phi(1)\right\rangle}_{1}+\nonumber\\
\underbrace{\left\langle\phi(1)\phi(2)\left|-\frac{1}{r_{12}}\right|\phi(1)\phi(2)\right\rangle}_{5\zeta/8}
\end{eqnarray}
El resultado es:
\begin{eqnarray} W=\underbrace{\left\langle\phi(1)\left|-\frac{1}{2}\nabla_1^2\right|\phi(1)\right\rangle}_{\zeta^2/2} \underbrace{\left\langle \phi(2)|\phi(2)\right\rangle}_{1} +\nonumber\\ \underbrace{\left\langle\phi(2)\left|-\frac{1}{2}\nabla_2^2\right|\phi(2)\right\rangle}_{\zeta^2/2} \underbrace{\left\langle \phi(1)|\phi(1)\right\rangle}_{1} + \nonumber\\ \underbrace{\left\langle\phi(1)\left|-\frac{-Z}{r_1}\right|\phi(1)\right\rangle}_{-Z\zeta} \underbrace{\left\langle \phi(2)|\phi(2)\right\rangle}_{1} +\nonumber\\ \underbrace{\left\langle\phi(2)\left|-\frac{-Z}{r_2}\right|\phi(2)\right\rangle}_{-Z\zeta} \underbrace{\left\langle \phi(1)|\phi(1)\right\rangle}_{1}+\nonumber\\ \underbrace{\left\langle\phi(1)\phi(2)\left|-\frac{1}{r_{12}}\right|\phi(1)\phi(2)\right\rangle}_{5\zeta/8} \end{eqnarray}