The following options discussed in this page are saved in the BlueBrick BBM file, therefore they are not really preferences for BlueBrick, but more Properties of your layout.
By double clicking on the layer tabs 10 you can gain access to the various configuration options which each layer provides. The options are different depending on what type of layer it is, but for all of them you can at least change the name of the layer, its visibility and its transparency. For the Area and Grid layer, you can also tune the paintbrush size and grid size.
Clicking on Edit > map background color... provides you with a pop up window from which you can select your desired background color. You can also change the background color through the Properties tab of the Map located in the bottom right, see the Map Properties section for more details. Note that layers are transparent and you can not set different background colors for each layer.