Set your path to Putty on Integration tab of Preferences dialog. Also since next version (within few days) WinSCP will search for Putty in Windows search path list (PATH environment variable).

Minor issue

By default WinSCP thinks putty.exe path is at C:\Program Files\PuTTY\putty.exe
But mine is at C:\bin\sshtools\putty.exe (I hate folder/file names with space, also the long names)

Instead of guessing path can we ask PuTTY developers to make it available thru their registry settings?
At start of PuTTY.exe they can add that registry entry if not exist/blank or update it when somebody save default settings.

In WinXP you can also able look at
HKEY_CURRENT_USER\Software\Microsoft\Windows\ShellNoRoam\MUICache
to find the putty path if it was started earlier

TIA
Biju
Similarly WinSCP should also put its path as a registry entry for other application to use.