Ballast serves to anchor the ties, which maintain alignment and gauge for the rails. Ballast also provides drainage. For track on which the railroad relies heavily for financial robustness, the drainage problem is serious. So, those tracks will have a raised roadbed, well compacted and leveled, and then ballasted. If your terrain is going to be essentially flat, then homasote caulked directly to the plywood is a good way to go IMO. If you intend some relief in the terrain, then the homasote should be adhered to the roadbed as it rises and falls.
For the more industrial tracks, yards, spurs, and so on, I would use N scale roadbed, or thinner cork than the homasote. Or, transition right down to the plywood if you wish. I have used long thin door jam cedar shims. Later, without forcing the flex track either up or down, but having it anchored at the diverging route of the turnout, I just lay it on the roadbed/plywood and let it conform and shape itself. I add one or two shims for support, but I often rely just on the ballast grains groomed to look right to support the flex track. Once it is glued, the ballast acts like a roadbed of sorts, and no one will know that you don't have a properly prepared roadbed. That's the way I did it for my recently built layout. I let the flex track tell me what it wanted to do, filled under it, or even built two plaster ramps in two cases. The plaster doesn't have to be carefully shaped initially. Just goop it into a couple of forms made with wood or plastic, and then sand it reasonably smooth.
