[guided]We need to check smoothness of $\Phi$ as a map into the total space $E$. Smoothness into the manifold $E$ can be checked after composing with local bundle charts whose domains cover the target over open sets covering $M$. Therefore we work over an arbitrary open set $U\subset M$ admitting a local product chart. Choose a smooth local vector bundle product chart
\begin{align*}
\tau:\pi^{-1}(U) &\to U\times \mathbb{R}^k.
\end{align*}
Inside this local product chart, each section $s_j$ becomes an ordinary smooth $\mathbb{R}^k$-valued function. More precisely, for every $j\in\{1,\dots,k\}$, define functions
\begin{align*}
b_{ij}:U &\to \mathbb{R}, \qquad i\in\{1,\dots,k\},
\end{align*}
by requiring
\begin{align*}
\tau(s_j(x))=\left(x,(b_{1j}(x),\dots,b_{kj}(x))\right).
\end{align*}
These functions are smooth because $s_j:U\to E$ is smooth and $\tau:\pi^{-1}(U)\to U\times\mathbb{R}^k$ is smooth.
Now collect these coordinate functions into a matrix-valued map
\begin{align*}
A_U:U &\to \mathbb{R}^{k\times k},
\end{align*}
where the $(i,j)$ entry of $A_U(x)$ is $b_{ij}(x)$. The $j$th column of $A_U(x)$ is exactly the coordinate vector of $s_j(x)$ in the product chart $\tau$.
For $a=(a_1,\dots,a_k)\in\mathbb{R}^k$, linearity of $\tau$ on each fibre gives first
\begin{align*}
\tau(\Phi(x,a))=\tau\left(\sum_{j=1}^k a_j s_j(x)\right).
\end{align*}
Because $\tau$ is fibrewise linear over $U$, this equals the coordinate expression
\begin{align*}
\left(x,\sum_{j=1}^k a_j(b_{1j}(x),\dots,b_{kj}(x))\right).
\end{align*}
By the definition of the matrix $A_U(x)$, the same vector is
\begin{align*}
\left(x,A_U(x)a\right).
\end{align*}
Therefore
\begin{align*}
\tau(\Phi(x,a))=\left(x,A_U(x)a\right).
\end{align*}
Thus, in the local product coordinates determined by $\tau$, the map $\Phi$ is represented by the map $U\times\mathbb{R}^k\to U\times\mathbb{R}^k$ given by
\begin{align*}
(x,a)\mapsto (x,A_U(x)a).
\end{align*}
This map is smooth because the entries of $A_U(x)$ are smooth functions of $x$ and matrix multiplication is polynomial in the entries of $A_U(x)$ and the coordinates of $a$. Since the open sets $U$ with local product charts cover $M$, $\Phi$ is smooth on all of $M\times\mathbb{R}^k$.[/guided]