When you are processing a file, you define what zoom level will be rendered.
By default, zoom levels are calculated based on the image resolution and its geolocation. There are defined minzoom and maxzoom levels, from which one can calculate how many tiles will be rendered.
Zoom levels in MapTiler Desktop Free/Start/Plus
Since Free/Start/Plus version of MapTiler Desktop can process only one file at a time, it has single spinbox for minzoom and maxzoom values.
Zoom levels in MapTiler Desktop Pro
In MapTiler Desktop Pro, you will get a separate dialog for setting zoom levels. It is available after georeferencing before rendering.
In this window, you can set zoom levels for each image. Zoom levels for all images are visible next to them (if you are in the All tab).
You can also set visibility for each image. By clicking on Up button, you move up selected image in the list. The image which is highest will have the highest visibility, the one which is just below will get the second highest visibility (which means the first image will be rendered in the final map over the second one if they overlap, but the second will be rendered over the third one in case of overlap) and so on.
On the top, you can see the All tab and another one for each zoom level group. This is useful if you have images on different zoom levels: here you can filter only images which are on specific zoom levels or zoom level groups (e.g. images with zoom levels 11-13).
Increasing maxzoom by 1 or 2 zoom levels is available and preferred. Further increasing would result in a damaged image (overzoomed).
When increasing maxzoom level, it is better to use Cubic B-Spline resampling method in Advanced Options.