I haven't upgraded my second installation yet (which is the one that does email tickets, etc) so this if for my 1.6ST install, but its may assist you. First thing I did was create a nightly.bat. Here are the (slightly modified) contents of my .bat file.
C:\Progra~1\PHP\php.exe -f c:\Inetpub\wwwroot\MYSITEDIR\api\cron.php
This should read PATH-TO-PHP-EXE -f PATH-TO-api\cron.php. I then created a shortcut to it. And setup Task Scheduler to call the shortcut every couple minutes.
By the way:
cron.php is for running on your webserver via cron or windows task scheduler.
rcron (API) is for if you are using cron or windows task scheduler on another server to trigger the process on your webserver.
Please let me know if you need anything else. :)