For general text you can use \raggedright and \raggedleft to align the material to the left and right, respectively. To align images inside a figure easily you can use the adjustbox package which allows you to add alignment keys to \includegraphics .
Multiple subfigures can be put in multiple rows by adding a \newline after one row is complete. For example, if you have four figures and you want to put them in 2x2 style, put \newline after two subfigures which will be placed in the first rwo. The command will create a new row for rest of the subfigures.
Next to reseting the counter for the figures:
\setcounter{figure}{0}
You can also add the "S" by using:
\makeatletter
\renewcommand{\thefigure}{S\@arabic\c@figure}
\makeatother
you can reset the figure counter with
\setcounter{figure}{0}
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