Just one possibility is with layer priority in my opinion.
That's right, but I think that's what Miki is trying to say. You can save your layers with
any
layer priority number you like for each layer combination.
For example, you may have a layer combination called 'Walls - Option A', where your walls layer may have an intersection priority number of 123. Then you may have a layer combination called 'Walls - Option B', where your walls layer may have an intersection priority number of 456.
Keep in mind that the layer intersection priority number itself has no priority, it just needs to be different than the number of the layer you don't want it to heal with.
Cheers,
Link.