A GARCH model generally is
\begin{aligned}
r_t &= \mu_t+\varepsilon_t, \\
\mu_t &= \dots, \\
\varepsilon_t &= \sigma_t z_t, \\
\sigma_t^2 &= \omega + \alpha_1 \varepsilon_{t-1}^2 + \dotsc + \alpha_s \varepsilon_{t-s}^2 + \beta_1 \sigma_{t-1}^2 + \dotsc + \beta_r \sigma_{t-r}^2, \\
z_t &\sim i.i.D(0,1), \\
\end{aligned}
where $\mu_t$ is some function of past information (maybe a constant, maybe some ARMA terms, maybe something else) representing the conditional mean of $r_t$, and $D$ is some distribution with zero mean and unit variance. The dependent variable of and the only necessary input into the model is $r_t$, and the model is that of the conditional distribution of $r_t$ (conditioned on past values of $r_t$ and possibly other variables). What makes the model a GARCH model is the particular form of the specification of conditional variance, $\sigma_t^2$.
Regarding your question, if $\mu_t=0$ then $r_t=\varepsilon_t$, and GARCH seems to model the conditional variance of $r_t$ "directly". If $\mu_t\neq 0$, then $r_t\neq\varepsilon_t$, and GARCH seems to model the conditional variance of $\varepsilon_t$ "directly" but of $r_t$ only "indirectly". However, this is a false dichotomy. Since we are conditioning on all past information, the conditional variance of $r_t$ equals the conditional variance of $\varepsilon_t$ by definition, so it is hard to make a mathematical distinction between them.
For more details, see "What is the difference between GARCH and ARMA?".