It's easy to create pop-up links via the content editor - just open the link dialogue box and choose 'Open link in...' = 'Modal Popup'. 

And it's pretty straight forward if you need to do this manually too. Just change the HTML code from:

<a href="/my/link/url/">the link</a>

To:

<a href="#" onclick="PagePop('/my/link/url/');">the link</a>