Actually, it is a bit more complex than you think. For example, when the user leaves the page and returns an hour later, you don't want to show the popup (overlay, because you can close a popup) again. This means that you need to save the acceptance in a cookie. The content files should also check whether the terms are accepted and whether the navigation frame is not shown. If the navigation is not shown, the content must show the EULA acceptance overlay as well.
You can use jQuery for RoboHelp (I've used it quite a bit.) In my experience, RoboHelp doesn't reformat the code when it is in an external script file. I use a lot of script files and I have never seen this behaviour before (though that doesn't mean it doesn't of course).
Such a requirement is a lot of work and the best I can do on the forum is point you in the right direction.
If you require professional support, contact me via my site: http://www.wvanweelden.eu/ and we can talk about your options. Note that this is not associated with my forum contributions nor is it in any way affiliated with Adobe.
I was thinking about put a <noscript> and replace the popup by a starting page with the same role.
A captive page to the first time the user connects, which asks for the agreement to the EULA, and if we respond "yes", a PHP session variable is generated, and the we are redirected on the help index.
If the answer is "no", we redirect user on our website.
The only problem is the following : Will it be possible to start a session on the helpdesk, and check if the session variable is ok. As you said no before, I'm afraid it's not possible ?
I'm a bit disapointed about RH ... again.
The best way I see is just to add a notice on every page that using the system means that you accept the EULA.
I made a temporary solution with JS, a confirm() pop-up, captured the returned value, with no code in the case of a true value, and with a redirect like : top.location.href="page.htm" if the returned value is false.