In the explorer interface, if you drag a file from the local PC to the folder displayed on the remote side, you'll get an overwrite confirmation request if that file already exists ("Remote file <whatever> already exists. Overwrite?").
However, if you drag a file to a folder that is not displayed (e.g. by dragging it either to one of the folders on the left hand side, or to a sub-folder displayed in the open folder on the right hand side), no such prompt is presented and the file is silently overwritten if it already exists.
I hope that's clear, but feel free to ask if you need clarification,