I hope this helps.
Michelle,
Since a pop-up is nothing more than another page. Usually coded in a way that will look somewhat decent when called to be open as a pop-up (instead of with the full browser window elements like the address bar, buttons, etc.). If you are opening a page in the pop-up window where you don't have access to its code, then you're out of luck. If the page is hosted in a server where you can include code at will, then simply add the script block on the page and you're done.
If the new window is hosted by a third party, you would need to ask them to include your Marketo instance's tracking script on it.
I guess that what I am saying is that it depends on what type of pop-up in order to give you a final answer.
Good luck!
Rafael