The current version of WinUAE has only one command line argument, to specify the configuration file.
From memory (as I am at work, which is not where my setup is) it is:
winuae.exe -f <config_file>
Given that to startup with a particular disk image, it must be in a config file, then I see two options for starting WinUAE from an FE:
(1) Have a config file (.uae file) for every game you intend on referencing from the FE. The files listed by the FE won't be the .adf files, but will be the .uae (config files)
(2) Write a wrapper / batch file to insert the correct adf filename into a generic config file, then run WinUAE with that config file.
(2) Would be relative simple, if the time were available. Its something I have been thinking about lately, but just need to find the time.
With regard to the wrappers, it should be a fairly trivial matter to use them to get WinUAE to load the config file. Its been a while since I looked at howards, but with mine you would simply set the pre rom text to be:
-f
Then setup the FE to reference the .uae files (As opposed to the .adf files) and you should be on your way.
If you need further help with this, let me know, and I can provide a sample wrapper config file.
Cheers
Martin
