XenForo Resource Manager keeps its files in attachment system and this add-on handles attachments perfectly. It's important to note that attachment full files are stored in internal_data, only the thumbnail files are stored in data therefore only the thumbnail files will be uploaded the remote servers.
You can upload using any tools, it doesn't matter. We often use the official aws cli.
The add-on processes all files in data directory (data, attachment thumbnail, etc.). You need to upload everything inside data to S3. For bdCache, you need to upload it too. Normally the old files inside bdCache are deleted automatically so it shouldn't grow much in size though.
Got it, thanks. I ended up going with your unmaintained avatar only storage plugin and it works perfect for what we need. Didn't want any other files to go into the cloud as it is, our cache is pretty big!