Yes! When you use a page in a funnel, FunnelFlux will redirect the user to it and establish a "session" for that visitor.
You can see the VID value we pass into page URLs or that our JS gets and puts into the URL. With this ID we know exactly what funnel a user is in and what page they are on.
When they then click on an action link to go somewhere, we will send them to the correct page even if your current page is in many funnels (remember, we already know exactly where the user is).
With our Javascript, you can embed code you get from the edit offer dialog, which includes a page ID, or code generated in the funnel builder, which contains a default funnel/node ID as well.
You don't need to worry about this JS code causing problems. When a page is loaded with our JS on it, the code will first check for an existing visitor ID, which it might find in the URL directly, page referrer, or cookies, and it will continue to use this -- so it won't override the existing user data and cause problems.