Multiple subscripts under different objects often require manual adjustment because of conflicting shapes.
Use a phantom.
\documentclass{article}
\usepackage{amsmath}
\begin{document}
\begin{equation*}
\sum_{u\in S}\sum_{v\in\overline{S}} c(u,v)
\qquad
\sum_{u\in S\vphantom{\overline{S}}}\sum_{v\in\overline{S}} c(u,v)
\qquad
\sum_{\substack{u\in S \\ v\in\overline{S}}} c(u,v)
\end{equation*}
\begin{equation*}
\sum_{u\in S}\sum_{v\in\bar{S}} c(u,v)
\qquad
\sum_{u\in S\vphantom{\bar{S}}}\sum_{v\in\bar{S}} c(u,v)
\qquad
\sum_{\substack{u\in S \\ v\in\bar{S}}} c(u,v)
\end{equation*}
\end{document}
I added alternative ways with \substack and \bar, which is generally preferable to \overline.

$$in LaTeX, see Why is\[ … \]preferable to$$? – egreg Apr 04 '20 at 09:10\documentclass{minimal}\begin{document}\[\sum_{u\in S}\sum_{v\in \overline{S}}f(u, v)\]\end{document}– Anthony Labarre Apr 04 '20 at 11:02minimalclass is not designed for such uses, better usearticle. – frougon Apr 04 '20 at 11:14