You can use a raw attribute in the yaml block to properly format the latex code used to specify affiliations. Here I modified the yaml block in the rticles template:
title: Short Paper
author:
- name: Alice Anonymous
email: alice@example.com
affiliation: a
correspondingauthor: true
footnote: 1
- name: Bob Security
email: bob@example.com
affiliation: b
- name: Cat Memes
email: cat@example.com
affiliation: b
footnote: 2
- name: Derek Zoolander
email: derek@example.com
affiliation: b
footnote: 2
address:
- code: a
address: |
```{=latex}
organization={Some Institute of Technology},
addressline={Street},
city={City}, state={State}, postcode={Zip},
country={United States}
```
- code: b
address: |
```{=latex}
organization={Another University},
addressline={Street},
city={City}, state={State}, postcode={Zip},
country={United States}
```
