As you are saying you need to track the click , So as per my thoughts
- one you can open the popup on the same window only if the popup contains the info to get studied and has dependencies over current screen, so there is no way user will get irritated as after doing stuff in popup he can close the popup , its better then getting blocked.
- second you can open the popup on new window only if the popup has info that might be read or studied later and has no such dependencies over current screen info, this will let the user a option of checking ti later while doing current stuff.