If you have installed macOS Sierra, you can now use tabbed windows in Cyberduck 5.2 or later. You might want to enable tabs by default when choosing File → New Browser by selecting in System Preferences the checkbox Dock → Prefer tabs when opening documents: Always. New browser windows and the transfer window will then be displayed in a single window frame with a tab bar. You can merge windows with View → Show Tab Bar and Window → Merge all Windows.
Refer also to Use tabs with apps on your Mac.
Amazon S3 Transfer Acceleration enables fast, easy, and secure transfers of files over long distances between your client and an S3 bucket. Transfer Acceleration takes advantage of Amazon CloudFront’s globally distributed edge locations. As the data arrives at an edge location, data is routed to Amazon S3 over an optimized network path. In general, the farther away you are from an Amazon S3 region, the higher the speed improvement (up to 300% faster) you can expect from using Amazon S3 Transfer Acceleration.