I read in Serre's "Lectures on $N_X(p)$" that when $X$ is a scheme defined over $\mathbb{F}_q$ (a finite field), the geometric Frobenius $F: X \mapsto X$ is defined by fixing every element of the topological space of $X$, and acting as $f \mapsto f^q$ on the structure sheaf. As a particular case, if $X$ is affine (say $Spec(\mathbb{F}_{q^n}[x,y])$), then "$F$ is the "standard Frobenius map" (on points): $(u,v) \mapsto (u^q,v^q)$." Why is that ? Doesn't the action on the structure sheaf implies that every element of $\mathbb{F}_{q^n}[x,y]$ is raised to the $q$-th power ? Also, I have seen other definitions of geometric Frobenius. (I have noticed related questions on MO, but the answers confuse me even more.)
Secondly, it is mentioned that the geometric and arithmetic Frobenius act in the same way on $X(\overline{\mathbb{F}_q})$. Can anyone explain this in some detail ?
Thanks !