WinSCP can be used to create and edit remote files, and perform custom commands on those files. For example, where the remote system is a Linux cluster, it can be used to submit jobs on that remote system. If that is all you need, then you may find that you don't often need to use a program like Putty, though the latter will be useful if you need a command session or GUI access.
Submit job qsub -j oe "!"
Check status qstat