I have all the settings right to generate pictures using Atlas, but I can't access the 'Controlled by Atlas' checkmark in the print layout. It's greyed out, and whatever I try I'm unable to change this. I have a shapefile as layer, and an XLS file as Coverage layer. No background. Any idea what I'm doing wrong?
In your question you state that you have a XLS file as the coverage layer. I suspect that this means your coverage layer is a table only, without any geometry information.
A geometryless table CAN be used as an atlas coverage layer (e.g. to iterate over text in the rows), but it can't be used to automatically set a map item's extent (since there's no geometry information in that table to set the extent to!). You should still be able to use the data defined scale/x min/x max/etc settings to setup the map's view, if your table has information present which would allow you to derive these values.