I'm reading page 2 of conditional probability. The author states that if $\text{Var(X|Y)}$ is treated as a random variable then the expectation is $\text{E[Var(X|Y)] = E[E[X^2|Y]] - E[E(X|Y)]^2}$
My question is what exactly does the expected variance mean as far as the the random variables, X and Y are concerned? An intuitive explanation would suffice.
$Y$ is a random variable. $X$ is taken to depend on $Y$ in some way (could be strong, could be nonexistently weak). The variance of $X$ given $Y$ is
Without more details about an assumed relationship between $X$ and $Y$, no more can be said that what you've quoted. (The expected variance in $X|Y$ is the difference between the expectation of (the expectation of $X^2|Y$) averaged over the distribution of $Y$s and the square of the expectation of (the expectation of $X|Y$) averaged over the distribution of $Y$s.)
(Actually, some more can be said under weak assumptions, but I bet (without checking) that most of this appears on the page(s) you are reading.)