Any suggestions on what is the best way to get a confirm delete dialog within a modal ? I don't think open modal on top of an other modal is the best way.
Apps handle this situation all the time, and you're correct pop-up/modal confirmations are not usually a good option.
Here's an example: A sales representative opens up a modal in order to delete a contact, a vendor, or whatever. On selecting submit a div is revealed asking "Are You Sure?" When the rep presses yes the delete goes through.
If the representative still has more actions to complete on the modal then the modal remains open. Depending upon your app there may be no need for the modal to remain open in which case the modal can close as well. Bear in mind, depending upon your users, and how this fits into their work expectations, the double action (form submission and closing the modal) may be very unsettling so it may make sense to tell the user that on submission the modal will close and he will be returned to original page.