A way to separate multiple table or figure environments in latex:

\newcommand{\beginsupplement}{%
        \setcounter{table}{0}
        \renewcommand{\thetable}{S\arabic{table}}%
        \setcounter{figure}{0}
        \renewcommand{\thefigure}{S\arabic{figure}}%
     }

Then, when your supplement starts, just add the line:

\beginsupplement

Voila! Instant “Table S1” and “Figure S1”. Enjoy.