Multiple layers are available only in MapTiler Desktop Pro (not in Free, Start and Plus versions).
With MapTiler Desktop, you can either merge multiple images together and create one big map overlay, combine images on different zoom levels which changes as the end-user will zoom through the final map or merge multiple MBTiles together.
Merge multiple images together to create a mosaic
You can also make a color correction to give all images unified seamless look.
Map created from four aerial images
Combine images on different zoom levels
You can also combine images on different zoom levels, so the final product will be a map where different layers change as the end-user zooms in and out. The procedure is similar to the example above, but with multiple layers (which mostly consists of images taken by different devices in a different time) is even more important to make a color correction to give the map unified seamless look.
Merge multiple MBTiles
MapTiler can also merge multiple MBTiles together. If you have an image you want to include in your map, process it first and render into MBTiles format and then merge with existing MBTiles file.