Sure can. Here's a couple possibilities I can think of:

1. You could create a page for each popup, then give each a custom theme which is really simple. Then you can open these pages in an iframe with your lightbox script

2. You can use the Popup add-on from the Marketplace. It takes a little bit to set it up, but I think that this will let you pull an "area" from a page, like the header, sidebar, or the content. This would let you create new pages for your popups and it will grab only the content and leave out the extras so it appears correctly, or you could put your popups in the global scrapbook and edit them there


Either way, it shouldn't be too painful, and your clients should still be able to edit them like they would other content