Hi,
I assume you are talking about this article? https://devcentral.f5.com/articles/tweaking-firepass-integrating-rsa-securid-via-webdav-customization.UqFnY_RDs_0
I'm not in front of my firepass right now but what you need to do is set the passcode field to be the third option so when you click on userid you type it in press tab and type in the AD password and then tab again which will bring up the RSA app.
The RSA app is triggered by the javascript "onfocus" attribute of the form input element. The code also goes ahead and submits the form for you after the passcode is passed back to the web page from the token app. You can modify the code to not do the auto submit and that will make it where they actually have to click the login button.
Please let me know if this helps...
Seth