I assume scenes are for different levels, but should I use them for menu screens or is there a specific tool for menu screens?
It depends on the usage.
If you have a menue that is shown upon the start of game ( e.g. main menue ), then it's quite obvious that you want to treat it as a scene. However, when you have simple little menu that is used quite often then it's not really wise to reload the scene each time. Especially when you're having some pause menu.
The general rule is that a scene is a thing that has it's own distinct processing regimen. If none of the logic running is the same as that of another part of the application, then they should be two distinct scenes.
OTOH, if for instance you are doing level flythroughs behind your main menu (think MineCraft), then you probably want to adapt your in-game scene, such that you e.g. have no player input, and menu overlays are present and active instead... because running the scene is a lot of logic you don't want to have to repeat.
For the main menu screens if you are using UnityGUI, you can use more than one camera for different GUIs, in one scene. For example, when you press Play at the start menu, the current camera turns off and another camera which shows, say a Car Selection menu, turns on. All these happen in one scene.