Layers
The layer buttons are located on the bottom right of the application window:

The layers are ordered from layer 10 through to layer 1, with layer 10 being the top layer ("closest" to the viewer). This is shown with the button labels of the current layer select buttons; L10 corresponds to layer 10, L9 corresponds to layer 9 and so on. To select a layer as the current layer, that is what you want to draw/fill/sample/move etc. on, click on the button that has the layer name as its label.
The background underneath all the layers is white and cannot be changed under normal operation; if you want a different background colour, then colour layer 1 to your desired colour.
To translate the view, press the up, down, left or right buttons on your keyboard. The scroll bars will be updated to the position of your view:

To reset the view to the origin (top left), press the O button on your keyboard.
Shown below is the layer 7 (L7) selected as the current layer:

To the left of the current layer select buttons are the layer visible buttons. Blue means that the layer is visible, white means that it is not:

To toggle visibility, click on the button:

You can reorder layers with shift up/down on your keyboard.
You can merge down the layers with ctrl m. It will add the contents of the layer on top of the layer directly below it. For example, pressing ctrl m whilst layer 10 (L10) is selected as the current layer will merge the contents of layer 10 onto the top of layer 9 and clear layer 10 to 0xFFFFFF.
You can copy down the layers with ctrl j. It will make the layer below the currently selected layer a duplicate of the current layer.
You can clear (reset to 0xFFFFFF) layers with ctrl delete.
Before clearing or doing anything destructive, it might be wise to back up your drawing.