You should not be asked to confirm file overwrite when uploading from editor. At least I'm not :-)
What version of WinSCP are you using? What is your editor settings (Editor tab of Preferences window)?
Please, if you could do two settings of 'No confirmations' property - one for classical file transfer and other one for remote files editing. The problem is, that I need to have confirmations turned on for classical file transfer (to prevent files overwriting and ...) but if I am editing some remote file (using ctrl-e) i need this turned off.
It is not comfortable to switch this everytime. And the biggest problem is, if I am editing some remote file (using external editor) and have confirmations turned on - I have problem to save this file twice because after first save operation WinSCP asks me if to overwrite and the file is "blocked". I don't want to switch everytime between WinSCP and editor after each Save.