First thing to notice is that the Poynting Vector is "redefine" when dealing with complex functions. This is something usually overlooked by books, Jackson's for exemple doesn't even bother changing notation to call attention to that, so if you don't read the text you can get confused.
So, if you have a eletromagnetic wave (in the vacuum):
$$
\begin{align}
\vec{E} (\vec{r},t) = \vec{E}_{0} \, \cos(\omega\ t - \vec{k} \cdot \vec{r})
\tag{1}\label{eq1}
\\
\vec{H} (\vec{r},t) = \hat{k} \times \frac{\vec{E}}{Z_{0}} \,,
\tag{2}\label{eq2}
\end{align}
$$
the Poynting Vector is:
$$
\vec{S} (\vec{r},t) = \vec{E} (\vec{r},t) \times \vec{H} (\vec{r},t) \ .
\tag{3}\label{eq3}
$$
Now, if we have the complex form of the fields:
$$
\begin{align}
\vec{E} (\vec{r},t)
&=
\Re \ [ \ \vec{\tilde{E}} (\vec{r},t) \ ]
=
\Re \ [ \ \vec{E}_{0} \ e^{ \ i \ ( \ \omega\ t \ - \ \vec{k} \ \cdot \ \vec{r} \ )} \ ]
=
\Re \ [ \ \vec{E}_{0} \ e^{-\ i \ \vec{k} \ \cdot \ \vec{r} } \ e^{ i \ \omega\ t } \ ] \\
&=
\Re \ [ \ \vec{\tilde{E}}(\vec{r}) \ e^{ i \ \omega\ t } \ ]
=
\frac{1}{2} \ [ \ \vec{\tilde{E}}(\vec{r}) \ e^{ i \ \omega\ t } + \ \vec{\tilde{E}}^{\, \bf*}(\vec{r}) \ e^{ -i \ \omega\ t } \ ] \,,
\end{align}
\tag{4}\label{eq4}
$$
where $\vec{\tilde{E}}(\vec{r})$ is the phasor (a complex function with phase and magnitude that change with position; it is time independent), we get:
$$
\begin{align}
\vec{S} (\vec{r}, t)
&=
\frac{1}{2} [ \vec{\tilde{E}}(\vec{r}) e^{ i \ \omega \ t } + \vec{\tilde{E}}^{\ \bf*}(\vec{r}) e^{ -i \ \omega \ t } ] \times \frac{1}{2} [ \vec{\tilde{H}}(\vec{r}) e^{ i \ \omega \ t } + \vec{\tilde{H}}^{\ \bf*}(\vec{r}) e^{ -i \ \omega \ t } ]
\\
&=
\frac{1}{2} \Re [ \vec{\tilde{E}}(\vec{r}) \times \vec{\tilde{H}}^{\ \bf*}(\vec{r}) ] + \frac{1}{2} \Re [ \vec{\tilde{E}}(\vec{r}) \times \vec{\tilde{H}}(\vec{r}) e^{ 2 \ i \ \omega \ t } ] \,,
\end{align}
\tag{5}\label{eq5}
$$
whos average in time is:
$$
\langle \ \vec{S} \ \rangle_{t} = \frac{1}{T} \int_{0}^{T} \vec{S}(\vec{r}, t) \ dt
=
\frac{1}{2} \ \Re \ [ \ \vec{\tilde{E}}(\vec{r}) \times \vec{\tilde{H}}^{\, \bf*}(\vec{r}) \ ] \,,
\tag{6}\label{eq6}
$$
that way you can define a "complex" Poynting Vector:
$$
\vec{S}_{c} \equiv \frac{1}{2} \ \vec{\tilde{E}}(\vec{r}) \times \vec{\tilde{H}}^{\, \bf*}(\vec{r}) \,,
\tag{7}\label{eq7}
$$
and the average of the Poyting Vector is the real part of this quantity:
$$
\langle \ \vec{S}(\vec{r},t) \ \rangle_{t} = \Re \ [ \ \vec{S}_{c} (\vec{r}) \ ]
\ .
\tag{8}\label{eq8}
$$
Finishing the calculation we get:
$$
\begin{align}
\langle \ \vec{S}(\vec{r},t) \ \rangle_{t}
&=
\frac{1}{2} \ \Re \ [ \ \vec{\tilde{E}}(\vec{r}) \times \vec{\tilde{H}}^{\, \bf*}(\vec{r}) \ ]
=
\frac{1}{2Z_{0}} \ \Re \ [ \ \vec{\tilde{E}}(\vec{r}) \times \hat{k} \times \vec{\tilde{E}}^{\, \bf*}(\vec{r}) \ ]
\\
&=
\frac{1}{2Z_{0}} \ \Re \ \{ \ [ \ \vec{\tilde{E}}(\vec{r}) \cdot \vec{\tilde{E}}^{\, \bf*}(\vec{r}) \ ] \hat{k} - [ \ \vec{\tilde{E}}(\vec{r}) \cdot \hat{k} \ ] \ \vec{\tilde{E}}^{\, \bf*}(\vec{r}) \ \}
\\
&=
\frac{1}{2Z_{0}} \ | \vec{\tilde{E}}(\vec{r}) |^{2} \ \hat{k}
=
\frac{1}{2Z_{0}} \ | \vec{E}_{0} |^{2} \ \hat{k} \,,
\end{align}
\tag{9}\label{eq9}
$$
as expected.
For a dichromatic wave:
$$
\begin{align}
\vec{\tilde{E}}_{tot} (\vec{r},t)
&=
\vec{E}_{0} [\ e^{i \ ( \ \omega_{1} t \ - \ \vec{k}_{1} \ \cdot \ \vec{r} \ )} + e^{i \ ( \ \omega_{2} t \ - \ \vec{k}_{2} \ \cdot \ \vec{r} \ )} \ ]
\\
&=
\vec{\tilde{E}}_{1}(\vec{r}) \ e^{i \ \omega_{1}\ t} + \vec{\tilde{E}}_{2}(\vec{r}) \ e^{i \ \omega_{2}\ t} \,,
\end{align}
\tag{10}\label{eq10}
$$
you can see by yourself that the time average operation will return zeros for the combinations of the time periodic exponentials, just like before. In the end:
$$
\begin{align}
\langle \ \vec{S}(\vec{r},t) \ \rangle_{t}
&=
\frac{1}{2Z_{0}} \ \Re \ \{ \ [ \ \vec{\tilde{E}}_{1}(\vec{r}) \cdot \vec{\tilde{E}}^{*}_{1}(\vec{r}) \ ] \hat{k}_{1} + \ [ \ \vec{\tilde{E}}_{2}(\vec{r}) \cdot \vec{\tilde{E}}^{*}_{2}(\vec{r}) \ ] \hat{k}_{2} \ \}
\\
&=
\frac{1}{2Z_{0}} \ [ \ | \vec{\tilde{E}}_{1} |^{2} \hat{k}_{1} \ + \ | \vec{\tilde{E}}_{2} |^{2} \hat{k}_{2} \ ]
=
\frac{1}{2Z_{0}} \ | \vec{E}_{0} |^{2} \ ( \hat{k}_{1} + \hat{k}_{2} )
\,,
\end{align}
\tag{11}\label{eq11}
$$
if the waves travels in the same direction $\hat{k}$:
$$
\frac{1}{Z_{0}} \ | \vec{E}_{0} |^{2} \ \hat{k} \ .
\tag{12}\label{eq12}
$$
Notes:
$\boldsymbol{\cdot}$ The direction of wave propagation and the direction of the wave vector can be different if the medium is not (lossless) isotropic [1].