The easiest way to add author affiliations is with the authblk package. If you add:
\usepackage{authblk}
to your preamble, you can then fill in the author and affiliation commands with the information you need, for example:
\author[1]{Alice Smith} \author[2]{Bob Jones} \affil[1]{Department of Mathematics, University X} \affil[2]{Department of Biology, University Y}
for a paper with two authors.