The ray transfer matrix for a gap is typically:
$$\begin{bmatrix} 1 & d \\ 0 & 1\\ \end{bmatrix}$$
If I know that my glass is a thickness $L$ does the ray of light that goes into it travel a distance $n' \, L$ where $n'$ is the refractive index of the glass? So would the $d$ inside the matrix change to $n' \, L$?
Close.
From https://en.wikipedia.org/wiki/Ray_transfer_matrix_analysis
The transfer matrix upon entering the glass is:
$$\begin{bmatrix} 1 & 0 \\ 0 & \frac1{n'}\\ \end{bmatrix}$$
The matrix inside the glass is:
$$\begin{bmatrix} 1 & d \\ 0 & 1\\ \end{bmatrix}$$
And upon exiting the glass it's:
$$\begin{bmatrix} 1 & 0 \\ 0 & \frac{n'}1\\ \end{bmatrix}$$
So multiplying together you get:
$$\begin{bmatrix} 1 & 0 \\ 0 & \frac{n'}1\\ \end{bmatrix} \begin{bmatrix} 1 & d \\ 0 & 1\\ \end{bmatrix} \begin{bmatrix} 1 & 0 \\ 0 & \frac1{n'}\\ \end{bmatrix}= \begin{bmatrix} 1 & \frac{d}{n'} \\ 0 & 1\\ \end{bmatrix}$$
This makes sense intuitively as the higher the index of refraction of your glass the less displacement you'll get.
If your starting and/or ending medium have index of refractions other than 1 then you'd need to modify the 1 in the corresponding fractions to get the corresponding transfer matrix.
No, you would use the actual thickness of the glass $L$. This is because your ray matrix should change the angle of the incoming ray at the boundary using Snell's law, and to calculate the propagation accurately beyond that, you will want to use the distance covered by the ray in the lab frame.
