Given an $n \times n$ matrix $A$, we can define a linear transformation $T: \mathbb{R}^n \rightarrow \mathbb{R}^n$ by $T(x)=Ax$.
We could also define a bilnear function $T: \mathbb{R}^n \times \mathbb{R}^n \rightarrow \mathbb{R}$ by $T(x,y) = y^TAx$.
Is there a relation between these two uses of the matrix?
Also, we could do the same thing with an $n \times m$ matrix and get a linear function $\mathbb{R}^m \rightarrow \mathbb{R}^n$ and a bilinear function $\mathbb{R}^m \times \mathbb{R}^n \rightarrow \mathbb{R}$. Is the relationship between using $A$ to define a linear function versus a bilinear function the same in this case?
Redefining symbols to avoid ambiguity: $T: \mathbb{R}^n \to \mathbb{R}^n$ is the linear map defined as $T(x) = Ax$ and $S: \mathbb{R}^n \times \mathbb{R}^n \to \mathbb{R}$ is the bilinear map defined as $S(x, y) = y^T A x$.
Constructing bilinear functions from linear functions using inner product
One way to understand $S$ is as composition of $T$ with the standard inner product $\phi: \mathbb{R}^n \times \mathbb{R}^n \to \mathbb{R}$ defined as $\phi(x, y) = y^T x$, namely
$$ S(x, y) = \phi(T(x), y). $$
This view allows us to notice some properties of $S$ based on properties of $T$ and known properties of $\phi$. For example, since $\phi$ is known to be non-degenerate, $S$ is non-degenerate if and only if $T$ is an isomorphism.
The construction is readily generalized to the $n \times m$ case by composing $T: \mathbb{R}^m \to \mathbb{R}^n$ with $\phi$.
Change of basis
For a fixed matrix $A \in \mathbb{R}^{n \times n}$ the construction above yields two functions: a linear function $T_A: \mathbb{R}^n \to \mathbb{R}^n$ and a bilinear function $S_A: \mathbb{R}^n \times \mathbb{R}^n \to \mathbb{R}$. The construction takes place in a fixed basis, but the resulting functions $S$ and $T$ are independent of basis, so it is natural to ask how their matrix representation changes under basis transformations.
It easy to see that the matrix representing a linear function transforms differently than the matrix representing a bilinear function. Let $B$ denote an invertible matrix describing a change of basis. Then
$$ T_A = T_{A'} $$
whenever $A' = B^{-1}AB$, i.e. the matrices representing a fixed linear map are similar. On the other hand,
$$ S_A = S_{A^{''}} $$
whenever $A^{''} = B^TAB$, i.e. the matrices representing a fixed bilinear map are congruent.
This shows that care must be taken when using matrix representations of linear and bilinear functions. Even when a linear function $T$ and a bilinear function $S$ are represented by the same matrix in one basis, it does not imply that they are represented by the same matrix in another basis (unless the basis transformation is orthogonal).