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Applications Integration Tab (Preferences Dialog)
The Applications Integration tab on the Preferences dialog allows user to configure how WinSCP integrates with other applications, particularly with PuTTY.
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External Applications
Using PuTTY path box you can specify local path to PuTTY application that is used in Open in PuTTY function.
Check Remember session password and pass it to PuTTY checkbox to make WinSCP keep session password in memory and pass it to PuTTY when using Open in PuTTY function (using command-line parameter -pw). However better approach would be to use public key authentication together with Pageant.
By default WinSCP instructs PuTTY to open Telnet session if you are using FTP. Uncheck the Open Telnet sessions in PuTTY for FTP sessions to use SSH instead1.
Check Automatically open new sessions in PuTTY to automatically send all sessions opened in WinSCP also to PuTTY.
Further Reading
Read more about Preferences dialog and its other tabs.