I don't completely understand what you're trying to do, but I think a popup window might be somewhat of an issue if the user's browser automatically blocks popup windows. Plus, if you were trying to run a process in the popup window, the user could close it and no longer have a way to check on the process.
Would it be possible to use Ajax to call back to a web service that gives the page information about the process? You could give the user a way to make the Ajax call to check on the status of the process or just have it continually polling in the background.
Edit:
You said you weren't too familiar with Ajax. For the most part, there are libraries to handle all the of hard details. I'll recommend jQuery because that's what I've been using for a while now.
If you go the Ajax route you'll be able to contain everything on one page and make the updates you need to make when the Ajax call is successful. Depending on how you write the code, it should be pretty reusable if you do it right. It really depends on how specific the your needs on each page.
Take a look at the jQuery documentation though. It may have what you need already built into it. Otherwise, someone else might be able to suggest some reasons why their favorite JavaScript library works better for what you're trying to do.