What is the best way to upload large files

The speed depends on your upstream bandwidth and parallelism (concurrent multipart uploads/downloads). You may tune a parallelism and number of concurrent transfers in both tools.
Just with rclone it’s a little bit easier in my opinion, since you may provide it as an option for every try.
See

In FileZilla you need to change values in the UI in two different places:

  1. number of transfers in EditSettingsTransfers, Maximum simultaneous transfers; you can also provide limits for concurrent uploads and downloads here (parallelism)
  2. the number of concurrent connections you may tune in the connection itself, FileSite Manager → “your connection” → Transfer settings, Limit number of simultaneous connections

However, the result not always be the same, FileZilla uses an ancient uplink library and the FileZilla Team is procrastinating to update for years. Newer version of uplink library works faster, and rclone uses a more new version of uplink library.

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