QGIS Atlas generation for multiple map extents?

You assume correctly, that you need to have one feature for each map in thecovrage file. based on your image I would advise you to create a polygon layer, with 5 polygons, which represents the individual areas of interest. This layer would be used as the coverage layer. You can hide this layer so it does not show on the map.

If you have a point layer for each region, you could go to processing -> QGIS geoalgorithms -> vector general tools -> Polygon from layer extent. With this tool, you would create your polygons, merge them into one file and use it as a coverage layer. With this approach, which can also be a batch process, you could create reproducible results

A solution that i often use for this kind of task is to use a point layer as the coverage layer.

This point layer (let's say 'Atlas features') contains one point per area of interest and the attribute table is fill with some specific data like height, width, scale, orientation, name,... This value can then be used as parameters in the atlas generator to get output that exactly fit to the desired size, scale,...

Very useful when your atlas need to have different page format or scale.