If you would like to have an Appendix or a Supplementary Information section in your document follow the instructions below in order to reference your figures and tables correctly, using a separate numbering scheme.

Click on Settings (cogs icon) in the Toolbar and Edit Macros.

In the header.tex file, insert these lines:
\newcommand{\beginsupplement}{%
\setcounter{table}{0}
\renewcommand{\thetable}{S\arabic{table}}%
\setcounter{figure}{0}
\renewcommand{\thefigure}{S\arabic{figure}}%
}

Go back to your document, and in the place where you want the supplemental information section to begin, insert the following LaTeX snippet:
\section{Supplementary Material}
\beginsupplement

Export your document and enjoy labels as S1, S2, etc.

Please note you can change the S to anything (e.g. A, for Appendix) by modifying the snippet in the header.tex file.