Here you can find the InDesign template recently used for our preprint - see the original example at this link: https://www.biorxiv.org/content/early/2018/03/04/138412
The updated template has the bioRxiv logo close to the page number - see an example here: https://www.biorxiv.org/content/10.1101/2021.05.27.446040v1