a single territory can be apart of multiple bonuses. You simply tie a territory to whatever bonuses you want in the warzone map editor.
Look at this map: https://www.warzone.com/SinglePlayer?PreviewMap=98958
And look at the Bonus Titled: "United States of America". It is a Bonus that contains the territories that other, smaller, bonuses also contain. Yet at the same time, there is no visual separation between it and other Super Bonuses. At a glance you would not know it is there unless you clicked it's Bonus Object. This is 100% a valid approach, and an easy one to take. It assumes players will be taking the smaller bonuses and look around to see important-looking Bonus Objects that may overlap with the territories they already have.
An alternate approach is to design a visual way to distinguish an area occupied by a Super Bonus from others. This could be a gap between territories you then fill in with a background color to give the illusion of a large outline. You could stamp out a unique shape into each territory apart of the same Super Bonus. You could ensure that the regular Bonus colors within a Super Bonus are all of the same general color -just different shades and hues. These other ways take more time and thought ahead of time, but if you run the risk of visual clutter. The map above does not do these, and it has a clean look to it that is easy to read.
The choice is up to you!