The main case can be found in Milne's article specifically Theorems 1.13, 1.14 on page 310. The idea, briefly, is as follows: Given a sheaf $F$ on a variety $X$ over a finite field $k$, then over an algebraic closure $\bar{k}$ of $k$, the group $H^i_{et}(\bar{X}, F)$ becomes a $Gal(\bar{k}/k)$-module. There is a spectral sequence involving the $H^j(Gal(\bar{k}/k), H^i_{et}(\bar{X}, F))$ which converges to $H^n_{et}(X,F)$. This is true over any perfect field.
When you have duality over $\bar{k}$ (e.g. $X$ smooth proper and $F$ nice), combine it with duality in Galois cohomology (in this our case, the group is very simple) : $\hat{Z}$) to get duality over $k$. This is true over any perfect field. The duality theorems now reflect the $k$: if Poincare duality for $X$ of dimension $d$ over $\bar{k}$ pairs $H^i$ with $H^{2d-i}$, over $k$ the pairing will be between $H^i$ and $H^{2d +m -i}$ where $m$ is the cohomological dimension (assumed finite) of the Galois group ($m=1$ in the case of a finite field).
Hope this helps.
