Which protocols are suitable for certain use cases?

It is advantageous to choose the backup program, which does not require to communicate with the server, whether the backup files has been changed or not in the primary data storage. For example rsync program compares files modification time on the source and target location and then based on this comparison transfers the files. Backup software, which is keeping own index of backuped files, does not need to contact the target machine. The example of such a software is open source project Bacula.

In case, that the limitation factor for transfer speed is the amount of backuped files or the average file size is less than tens of MBs, it is preferable to agregate the files into the bigger files. We can use simple tools, which creates tar files, or backuping software, which can backup the data into the virtual tapes, typically a few GB. The example of such a software is open source project Bacula

Minimal size o migrable file is 64 kiB, i.e. files smaller than 64 kiB are not migrated to the tapes and remain on a disc tier.

Please do not rotate files, which has been already backuped. In case you will upload your data and you will continuously rewrite them or move the, will cause difficulties with backups. It means that your data will not be migrated to the tapes and thus it cannot be backuped.

To select suitable protocol for your usecase, you can use services and protocols overview with recommendations.
In case you need additional encryption, you can use ENCFS.
Additional tutorial, how to use full potential SSH and SSH - Options for user authentication.