Try it.

You're going to be seeing this:
Error: To use darkcoind, you must set a rpcpassword in the configuration file:
/home/stu/.darkcoin/darkcoin.conf
It is recommended you use the following random password:
rpcuser=darkcoinrpc
rpcpassword=FgS1HunBZZjp71789svfbkDB56gvzdiuygEq7QxedJgtro6Sw47L
(you do not need to remember this password)
The username and password MUST NOT be the same.
If the file does not exist, create it with owner-readable-only file permissions.
It is also recommended to set alertnotify so you are notified of problems;
for example: alertnotify=echo %s | mail -s "DarkCoin Alert" admin@foo.com
Nope

, you simply add
>E:\darkcoin/darkcoind -rpcuser=darkcoinrpc -rpcpassword=FgS1HunBZZjp71789svfbkDB56gvzdiuygEq7QxedJgtro6Sw47L -testnet=1
Ofcourse, any conf file in the blockchain folder must not exist in this case, or else the daemon will still go looking for it after it starts. (and possibly override your parameters. I am not sure, have not tested this case, I keep no conf file)
As I said, you can completely ommit the conf file IF you have
direct shell access possibility to the daemon. (which is key)
I just tested it again, and it works.

The thing to understand here, is that this command is not written somewhere... it's a shell command call that the frontend.exe is making on the fly, it does not need a textfile somewhere, hence no need for a conf file.
So the frontend would make commands like this for every possible thing a darkcoin wallet is supposed to do, and recieve results back from the daemon, and use the beautiful darkcoin GUI to make it look sexy.