By default WinSCP transfers files on foreground. This way it can use one connection to the server only all the time, however during the transfer you cannot use Altap Salamander for any other task. Alternative way is to use background transfers.
Transferring Files on Background
To instruct WinSCP to perform the transfer on background, check Transfer on background on transfer options dialog before the transfer. If you do not use the dialog or want to transfer file on background by default, check Transfer on background by default on Background & Resume tab of Preferences dialog.
Once you instruct WinSCP to perform the transfer on background, separate transfer progress window is shown, WinSCP opens separate SSH connection to the server using the same session option as used for the main session. Once the transfer finishes the connection is kept on background and reused for future transfers.
Once the background transfer finishes, the target directory is reloaded (still on background) and content of the respective file panel is refreshed.