To create and assign boundary conditions to these surfaces:
In the Physics tab, ind the Physics section in the Physics Checklist.
Expand any physics you've created to view the Boundary Conditions section.
Click the + symbol to the right of the Boundary Conditions section.
From the dropdown menu that opens, you can select the type of boundary condition to create. The options available will vary based on the physics you're creating boundary conditions for.
Fine-tune the specifics for that boundary condition, explained here.
Scroll to the bottom of the properties panel to choose the surfaces to apply the boundary condition to by clicking on the box and selecting surfaces from the Geometry panel. Click anywhere outside the box to save.
Note: If one or more surfaces is already selected prior to clicking on the + symbol, those surfaces will be automatically assigned to the new boundary condition.
You can also assign a boundary condition to all remaining surfaces that do not have one by clicking on the Boundary Conditions section and selecting the Define All dropdown.
Once all surfaces have been assigned boundary conditions, the red dots will disappear.