Transfer Options Dialog
Transfer options dialog appears before transfer (upload or download) actually starts, so you can set your transfer options. The initial options are determined by your preferred default transfer options. In preferences you can suppress the dialog at all for uploads, not to have to confirm two boxes for each transfer.
The dialog slightly differs for uploads and downloads.
Target Directory
For downloads, use the box at the top of dialog to set destination directory and operation mask. You can change the destination to remote path to change the operation into Move/Duplicate.
For uploads, the destination is set already by the Copy box shown before Transfer options dialog and cannot be changed.
The destination directory is by default the current working directory (local for downloads and remote for uploads).
If you omit the operation mask, you must still include a trailing
slash / (for upload) or backslash \ (for download). Omitting the operation
mask is the same as using mask *.*.
Transfer Settings
Transfer settings box shows current transfer settings.
To change the settings, use Transfer settings button (alternatively you may double-click Transfer settings box).
Additional Options
The New and updated file(s) only checkbox makes WinSCP ignore files in source directory for which there exist file in the target directory with the same filename and the same or newer timestamp. The option is not available for uploads with SCP protocol. Make sure WinSCP can correctly convert timestamps from local conventions to remote server conventions and vice versa before using the option.
The Use same settings next time checkbox makes your options become default transfer options. It has the same effect as changing default transfer options in preferences.
For uploads you will have additional checkbox Do not show this dialog box again to disable the dialog for further transfers. You can always revert this in preferences.
Use Transfer on background checkbox to instruct WinSCP to perform the transfer on background.