Ditch the desktop shortcut
You can add command line arguments to the shortcut. No need to create a batch file.
-disableharddrivesafetycheck
You shouldn't need this more than once. If the CF card is already partitioned on the Amiga, WinUAE will accept it without disabling the safety check. Disabling the check only makes it easier to destroy your Windows harddrive.
Also starting with Vista, WinUAE won't reliably write to the CF card if it had a drive letter before. You should rather clean the disk for example with diskpart and then use it in WinUAE without -disableharddrivesafetycheck.
Getting the Ideal setup
You could simply select your preferred Amiga model from the Quickstart panel.
