I'm not sure which version of Windows you are using, but, under Windows 9*, you need to add the following line at the very end of your autoexec.bat file:

set PATH=%PATH%;C:\Perl\bin
[download]

where C:\Perl\bin is the path to your perl bin directory. Save autoexec.bat and reboot your computer. This is basically what you were trying to accomplish from the start and will allow you to avoid using a separate batch script and/or the addition of flags such as '-S' to your perl script.
Doing this on other Windows versions is similar, but for example with Win2K, the setting is made under 'Control Panel | System | Advanced | Environment Variables'.
HTH,
Chris
UPDATE: Or I need to read the question more clearly.