To set the syntax directory on the command line use "-s"

This is not documented - I learned it today from Sangil Kim, the author of
EditPlus. He is aware it is not documented, and I'm sure, will correct that in a
later version.

Templates, auto complete (*.acp), clip text (*.ctl), and syntax (*.stx) files
are all in the syntax directory.

For example, here is a shortcut to use the following:
ini directory: c:\projects\ini\number1
working directory: c:\projects\code\number1
syntax directory: c:\projects\templates\number1

"c:\Program Files\EditPlus 3\editplus.exe" -i c:\projects\ini\number1 -d
c:\projects\code\number1 -s c:\projects\templates\number1

The syntax and ini directories may be the same. But you should put both on the
command line.

Hope this helps,
Frederick