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I'm currently working on a small shop inside a website.
To keep the shop simple and clean there will open a pop-up when the user adds a product to their cart (to specify the product). The thing is that with some elements I need a second pop-up or a notification where the user can also customize things in. (Like downloading a template.)
To get a good ux I don't want a pop-up in a pop-up, a regular pop-up is not a option because they need to be interactive.
It sounds like your highest priority is having a site with a design that looks good. I think you should rethink what the site will be like to use and give that a higher priority. I've seen some great sites graphic design wise which I never see again simply because their UX is bad. Your design may be breathtaking beautiful and amazingly clean, but if it isn't usable you're going to drive people away.
Maybe you can explain what you are trying to achieve with your site and ask another question where we can give suggestions on how to achieve your goal for customers. That way I think we can give you more constructive advice.
Pop-ups are often blocked by browsers, so you are immediately going to loose anyone with pop-ups blocked (like me). You recognise that pop-ups in pop-ups are a bad idea already, so all I can say is that you're right.
