There are exact formulas for the automorphisms, for example in The Arithmetic of Elliptic Curves Appendix A, proof of Proposition 1.2. From those you can write down explicitly the action of $\text{Aut}(E)$ on $\omega=dx/(2y+a_1x+a_3)$. Here's the characteristic 3 case. $E$ has a Weierstrass equation of the form
$$ E:y^2=x^3+a_4x+a_6. $$
(In characteristic 3, this curve has $j(E)=0$.) Then $\text{Aut}(E)$ is the set of automorphisms of the form
$$ x\mapsto u^2 x+r\quad\text{and}\quad y\mapsto u^3y $$
with $(u,r)$ satisfying
$$ u^4=1\quad\text{and}\quad r^3+a_4r+(1-u^6)a_6 = 0.$$
So in this case, $\omega=dx/2y$ and the map $\phi_{u,r}$ associated to $(u,r)$ acts via
$$ \phi_{u,r}^*\omega = u^{-1}\omega. $$
To answer your second question, the group scheme structure is
$$ \text{Aut}(E)=\frac{k[u,r]}{\bigl(u^4-1,r^3+a_4r+(1-u^6)a_6 \bigr)}.$$
The calculation for characteristic 2, which I will leave for you, is similar.