I assume that you are talking about the changes in P, and P/E being uncorrelated, rather than the values themselves, since you are going to be simulating the increments in your GBM or AR process.
It seems reasonable to assume that increments in price and earnings are correlated (i.e. if earnings increase, the price will probably go up). And since P/E is a simple function of P and E, its relationship with P will be determined by the relationship between P and E.
The increments of P/E are given by
$$
\Delta (PE) = \frac{P}{E}\left( \frac{\Delta P}{P} - \frac{\Delta E}{E}\right)
$$
and so (abusing notation a bit) the covariance between P and P/E is
$$
\begin{align}
\mathrm{Cov}(\Delta P, \Delta PE)
& = \mathrm{Cov}(\Delta P, \Delta P) - \mathrm{Cov}(\Delta P, \Delta E) \\
& = \sigma_P^2 - \rho \sigma_P \sigma_E \\
& = \sigma_P \left( \sigma_P - \rho \sigma_E \right)
\end{align}
$$
therefore the increments in P will be uncorrelated with the increments in P/E if you have $\sigma_P = \rho \sigma_E$.
Since price volatility is generally higher than earnings volatility ($\sigma_P > \sigma_E$) and correlation is obviously less than one, this relationship will not hold in general, and you should expect the increments of P/E to be positively correlated with the increments of P.
Edit: I confirmed this with data, using quarterly price and earnings data for the S&P 500 from 1970 to present, and observed around an 80% correlation between log changes in price, and log changes in price-to-earnings.