You would need to use a Windows Adapter instead of the web adapter to supply any arguments. They are functionally the same though, so everything else will work the same. In your Path Property, set this to the full path to launch iexplore.exe on your machine (usually C:\Program Files (x86)\Internet Explorer\iexplore.exe). In the Arguments property, you'll enter the following;

"http://www.Whatever_URL_You_Want.org" -extoff -noframemerging

The extoff will turn off add-ons

the -noframemerging is what the web adapter uses to ensure it launches in a separate window (and therefore process so it can be hooked by this adapter instead of appearing under an existing IE instance).

If you have already interrogated a bunch of controls and want to convert your web adapter to a Windows adapter, that is possible via editing the XML. The easiest way to do that is to create a new Web adapter and a new Windows adapter and use a comparison tool to see what is different. Once you identify what is different, you can practice changing the XML in this simple solution until it works.