Modern understanding Darwin's "correlation of variation"
One must not confound a phenotypic variance-covariance matrix (usually called $P$) and a genetic variance-covariance matrix (usually called $G$) for a set of phenotypes. The mutational variance-covariance matrix is also a common concept (usually called $M$). There are a lot of papers on the evolution of the G-matrix (and related matrices).

In the abstract of Roff (2000), you can find the equuation

$$\Delta\bar z = GP^{-1}-S$$

, where $\Delta\bar z$ is the vector of mean responses, $G$ (often just called the G matrix) is the matrix of additive genetic variances and covariances, $P$ is the matrix of phenotypic variances and covariances and $S$ is the vector of selection differentials.

You will find much more by just googling "evolution of G-matrix"