First select the local files or directories you want to upload. Make sure that local panel is still active and use
command Files > Copy (or press
Before the upload actually starts, the transfer options dialog will show. There you will have a chance to change the transfer options or the target directory. The target directory is by default the current remote directory.
If you use Files > Move (or press
F6 key), the files will be moved to remote directory (i.e.
transferred and deleted from local directory).
Upload on Background
By default the upload starts on foreground, blocking the WinSCP window until it finishes. Learn how to schedule the background transfer.
Preserving Overwritten Remote Files
You can setup remote recycle bin to backup files that you overwrite during upload.