You can disable a scene in Custom Editor by selecting the scene and clicking on the Disable Scene button on the right side. You can re-enable a disabled scene by selecting Enable Scene button.
You can remove a scene in Custom Editor by selecting the scene and clicking on the Remove Scene button on the right side.
To edit items in a scene, you need to select it by clicking on it on the left hand side. Once your scene is selected, all items in that scene are listed on the right hand side.
To add a New Scene to your Custom Project, you need to click Add New Scene button at the bottom of the scenes. You can also choose to add new scene after or before your selected scene by clicking the arrow button next to Add new Scene Button and...