In order to bake materials with multiple slots, you have to make sure that each material is assigned to a different island in your UV map with enough margin.
In edit mode you can select the island that you want to use with the second material (you can select islands by pointing at them and pressing “L” in the keyboard), then with the SLOT 2 selected click the “Assign” button to assign that slot to your selection.
Now the baking process starts. First we add the sockets from the slot 1 to the baking queue (same as in the regular baking process):
Once you have all the maps paired you can adjust your baking settings and click bake:
And you now have the combined bake of the 2 slots in 1 material