# bmatrix: how to align elements' subscripts?

To align the 4 terms on their subscripts, I suggest you combine a bmatrix*[r] environment (provided by the mathtools package) with a \mathrlap{-} instruction (also provided by the mathtools package).

Update: to perform vertical alignment of the k subscripts in the first row, I suggest you provide add a \vphantom{-} superscript term to \mathbf{C}_k term in the upper-right cell.

The result of the adjustments is shown in the lower matrix:

\documentclass{article}
\usepackage{mathtools} % for bmatrix* env. and \mathrlap macro
\begin{document}
$\begin{bmatrix} \mathbf{P}^{-}_{k} & \mathbf{C}_k \\ \mathbf{C}_k & \mathbf{S}_k \end{bmatrix}$

$\begin{bmatrix*}[r] \mathbf{P}^{\mathrlap{-}}_{k} & \mathbf{C}^{\vphantom{-}}_k \\ \mathbf{C}_k & \mathbf{S}_k \end{bmatrix*}$
\end{document}

Here are two possibilities:

\documentclass{article}
\usepackage{amsmath}

\begin{document}
$\begin{bmatrix} \mathbf{P}^{-}_{k} & \mathbf{C}^{\vphantom{-}}_k\\ \mathbf{C}_k & \mathbf{S}_k \end{bmatrix} \begin{bmatrix} \mathbf{P}_{k}\llap{{}^{-}\mkern -3mu} & \mathbf{C}_k\\ \mathbf{C}_k & \mathbf{S}_k \end{bmatrix}$
\end{document}

Note: the second method uses manual adjustment for the horizontal position of the minus exponent (see the \mkern -3mu).