You can specify your parameters to fs.exe in a configuration file, as an alternative to the command line.
If you give no parameters on the command line, then fs.exe looks for a configuration file. By default it looks for a file called fs.cfg in the Fileshare directory, that is, the directory where you started fs.exe. You can use the /cf parameter to specify a different path and/or filename.
For example, you could have a configuration file c:\fsdir\fsconf.cfg containing:
/s server1 /tr f
and start your server server1, from your application command prompt, by entering the command:
fs /cf fsconf.cfg
Another example: you could have a configuraiton file c:\fsdir\fs.cfg containing:
/s server1
and start your server by entering:
fs