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The answers are all in the documentation, which should be available wherever you got the kixcrypt exe.
In fact the GUI should be there as well, which would have saved you a bit of grief, as it contructs the command line for you.
There is a newer version of KiXcrypt which I will try to make available again - I just need to geat my lazy arse shifted and set up a new site to download from as I lost the old one.
The new version includes support for passing command line variables, and a more secure method of passing the primary script.
You don't *have* to include kix32.exe with the "-f" switch. If is is on your PATH it will be executed automatically. If it is in a fixed location like your utils directory or a file share you can use the "-e" option to set the path explicitly. The encrypted exe is (of course) much smaller without kix32 compiled in.
However the nice thing about including the exe in the package is that you can be sure that you are running the interpreter and not some Trojan Horse that a tricky customer is using to grab your script.
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