Normally presets will be listed in the image you posted when you select a tool. For example the crop tool will have multiple option in that list allowing you to easily choose from presets that you use all the time.
If this is blank no matter what tool you choose, it is possible the preference file is corrupted, but we can get to that later.
Lets work on your layers post your screen with the layers panel open so that we can see what is going on.
Besides what Trevor told you, you can also select multiple layers, if layer 1 and the background layer are selected then what you do will be applied to both of them, assuming it can do so. some commands can not be applied to a background layer as they may require transparency or features that are available to just layers. In that instance the background layer can be unlocked to gain access to those commands. Dragging the padlock to the trash can will unlock the background layer.
When using the spot healing brush take a look at the top tool bar and see if it will be applied to a single layer, all layers, etc like Trevor mentioned.