Yes, it will depend on exactly what you are trying to achieve. If you require a separate "html" or "dhtml" window Wise Pop-Up will be an easy solution. If you wish just for a flash pop-up windows within the parameters and limits of the tour "stage" than you will simply do this within Tourweaver.
Daniel, I'm sure you have already resolved this issue but here is an example of what I think you want. This is my test tour where I am trying all the new features.