Possible to have a subtractive mesh/brush only affect specific meshes/brushes

I have a cylinder brush with a cube brush inside of it. I would like to create a subtractive cylinder to make a tube from the first cylinder, but I dont want it to affect the cube inside.

Is this possible through grouping? If this is possible, how would i set this up?

Yes, this is possible. What you will need to do is create an additive cylinder BSP. Then add a subtractive brush that is slightly smaller to the already called Additive Cylinder. Then add a box BSP. This system works on a stack so if you add the cube before you add the subtractive brush then the box will disappear. If this ever happens with additional BSP brushes then simply move the brush outside of the subtractive area and move it back in. This brings the other BSP to the top of the draw list. Now, you cannot add another subtractive brush after this. For instance if you added a second subtractive brush after the first the second subtractive brush will take priority.