This sounds like a case for learning how to correctly use layers (tags since 2020). ALL edges and faces should remain with Layer 0 (Untagged) assigned to them. Layer 0 (Untagged) should always be kept active. Only assign layers (tags) to groups and components.
From looking at your model it appears you are expecting layers to provide separation between geometry. They don’t If you remove the top face of your cylinder you will see that the shapes you’ve drawn on the side don’t have and backs.
If you want them to be objects in their own right, you should first make the cylinder a group and then outside of the group, draw the shapes and extrude them. And with Joint Push/Pull make sure you choose the setting to thicken the extrusion.
Here I’ve made a group for the cylinder. Then added the shapes on the outside of the cylinder and made each one of those a group. The grouping is what keeps them separated from each other.
I’ve also created layers(tags), one for the cylinder and another for the applied shapes. With the one for the cylinder turned off, you can see that the shapes have backs.