I select "Layer" from the menu and scroll down to "Flatten Image." After I do this I save this as a new .JPG file. I save it as the highest quality, which unfortunately tends to be large (meaning people on slow connections will have a while to load the comic every M-W-F), but I've seen how it looks if I don't so I just prefer the better quality version. I save this copy under a folder called " Finished - JPG (Completed; Final)."

And that's how I do the comic!