In general, all you need to do is book a multi-city itinerary with the two segments BOG-PTY then PTY-EWR on copaair.com. However, note that CM does not fly PTY-EWR, that's United. Frankly, I wouldn't trust CM's advertised "free stopover" as anything real at all. As in, instead of the "same price" they mention, it might actually be cheaper to book the two segments via other means. I'd start with google flights and consider purchasing individual tickets from each airline's website.