First, pandoc has to be installed. This can be done several ways e.g., your package manager, conda, etc.
Next, get pandoc-scholar. The project repo is located at https://github.com/pandoc-scholar/pandoc-scholar.
To use pandoc-scholar, first clone the repo. Then, set the environmental variable PANDOC_SCHOLAR_PATH in your shell environmental control file to point to the location of the repo e.g.,
export PANDOC_SCHOLAR_PATH="/Users/orson.welles/pub/pandoc-scholar"
Next, install pandoc-xnos (https://github.com/tomduck/pandoc-xnos) to incorporate proper figure, table and equation referencing. This is done via pip.
Finally, in the directory where the source document resides, modify the Makefile appropriately. This can change depending on the template, bibliography and yaml header of the document. The bibliography should probably be specific to the project for neatness. To help, there is a way to back out the unique references from an .aux file if natbib is used – see https://pandoc-scholar.github.io/.