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Transfer Queue/Background Transfers
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 WinSCP for any other task. Alternative way is to use background transfers.
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Transferring Files on Background
To instruct WinSCP to perform the transfer of background, check Transfer on background (add to transfer queue) on transfer options dialog before the transfer. If you do not use the dialog or want to transfer file on background always, check Transfer on background by default on Background tab of Preferences dialog.
Once you instruct WinSCP to perform the transfer of background, the transfer is added at the end of transfer queue. WinSCP by default performs at most 2 background transfers at once. If you schedule more transfers, they will wait in the queue until some transfer is finished. For each background transfer 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.
You can change number of simultaneous transfers on Background tab of Preferences dialog. You can also allow WinSCP to process particular transfer despite the limits.
Once the background transfer finishes, the target directory is reloaded (still on background) and content of the respective file panel is refreshed.
Controling the Queue
Once you have your transfers sheduled, you can use queue list to manage them.