[guided]We start with a smooth section $A$ of the Hom bundle. This means that for every point $p\in M$, the value $A(p)$ is a linear map $A(p):E_p\to F_p$. Thus the only possible bundle map associated to $A$ is obtained by evaluation on the fibre. Define $\Phi_A:E\to F$ by $\Phi_A(v)=A(\pi_E(v))(v)$ for every $v\in E$.
This formula is well-defined because if $v\in E_p$, then $\pi_E(v)=p$, and $A(p)$ has domain $E_p$. Therefore $A(p)(v)\in F_p$.
Now we verify that $\Phi_A$ is a vector bundle map covering $\operatorname{id}_M$. For $v\in E_p$, the image $\Phi_A(v)=A(p)(v)$ lies in $F_p$, so
\begin{align*}
\pi_F(\Phi_A(v))=p=\pi_E(v).
\end{align*}
Hence $\pi_F\circ \Phi_A=\pi_E$, which is exactly the statement that $\Phi_A$ covers $\operatorname{id}_M$. For fixed $p\in M$, the restriction $(\Phi_A)|_{E_p}:E_p\to F_p$ is the map $v\mapsto A(p)(v)$ and is linear because $A(p)$ is an element of $\operatorname{Hom}(E_p,F_p)$.
The remaining point is smoothness. Smoothness of a bundle map is checked in local trivializations. Fix $p_0\in M$, and choose an open neighbourhood $U\subset M$ of $p_0$ over which both vector bundles are trivial. Let $\tau_E:\pi_E^{-1}(U)\to U\times \mathbb{R}^r$ and $\tau_F:\pi_F^{-1}(U)\to U\times \mathbb{R}^s$ be smooth local trivializations, where $r=\operatorname{rank}E$ and $s=\operatorname{rank}F$. These induce a trivialization of the Hom bundle by representing a fibre map $B:E_p\to F_p$ as the linear map between the model fibres. Explicitly, $\tau_{\operatorname{Hom}}:\operatorname{Hom}(E,F)|_U\to U\times \operatorname{Hom}(\mathbb{R}^r,\mathbb{R}^s)$ sends $B$ to $(p,\tau_{F,p}\circ B\circ \tau_{E,p}^{-1})$. Here $\tau_{E,p}:E_p\to \mathbb{R}^r$ and $\tau_{F,p}:F_p\to \mathbb{R}^s$ are the fibrewise linear isomorphisms obtained from $\tau_E$ and $\tau_F$.
Because $A$ is a smooth section, its local representative in this Hom-bundle trivialization is a smooth map
\begin{align*}
a:U&\to \operatorname{Hom}(\mathbb{R}^r,\mathbb{R}^s)
\end{align*}
satisfying
\begin{align*}
\tau_{\operatorname{Hom}}(A(p))=(p,a(p)).
\end{align*}
Now take a vector $v\in E_p$ and write $\tau_E(v)=(p,x)$ with $x\in \mathbb{R}^r$. Since $a(p)$ represents the linear map $A(p)$ in the chosen trivializations, the image $\Phi_A(v)=A(p)(v)$ is represented in $F$ by
\begin{align*}
(p,a(p)x).
\end{align*}
Thus the local coordinate expression of $\Phi_A$ is the map $U\times \mathbb{R}^r\to U\times \mathbb{R}^s$ given by $(p,x)\mapsto (p,a(p)x)$. This map is smooth because $a:U\to \operatorname{Hom}(\mathbb{R}^r,\mathbb{R}^s)$ is smooth and the evaluation map $\operatorname{Hom}(\mathbb{R}^r,\mathbb{R}^s)\times \mathbb{R}^r\to \mathbb{R}^s$ given by $(T,x)\mapsto T(x)$ is a smooth finite-dimensional bilinear map. Since every point of $M$ has such a neighbourhood $U$, the map $\Phi_A:E\to F$ is smooth globally.[/guided]