Kajatar,
Firstly welcome to the wonderful world of Layers in TS12 (and 2009, 2010) - a source of many arguments in these forums and much pain. Personally, I love layers but they do have bit of a learning curve.
Any layer you create can be easily deleted - use the layer tool (looks like a layer cake), select the layer from the list (the top group are route-layers and the bottom group are session-layers - another source of confusion until you get used to the concept). Then click the delete icon (it looks like an "X"). Any layer that is named route-layer or session-layer are the default layers that will always be present in any layout, so don't delete them.
Be aware that it is impossible to delete all your layers - a layout must have at least one route-layer and one session-layer to work.
My general advice about layers is to put all the track, tunnels, bridges, signals, switches and industry active assets into the route-layer - it will make your life so much easier. Scenery items (trees, buildings, etc) can also go into the same route-layer or into another layer (either route or session).
Session layers are used when you are creating a layout that will have a number of different session or themes - e.g. a passenger service session, and a coal or heavy freight session. In this situation you would put the different consists into a session-layer in your different sessions. If all this seems to be another language then don't worry. Experiment, try things with the layers to see what they do - but make backup copies of your work first.
Peter Ware