Now is the time to figure out, just how much below track level do you want the absolute deepest part of the layout -- river bottoms, culverts, trenches, gravel pits, whatever -- to be? You don't want bare plywood to be the bottom of a river etc but a light coating of sculptamold, as little as 1/16" can disguise the tell tale wood grain patterns. A little advance planning now will help you decide what you need on top of the plywood.
Stated another way are you modeling fairly flat Illinois/Wisconsin grainbelt terriory, or deeper river valleys or mountains? And don't forget that sidings are supposed to be slightly lower than the main line. Get out the scale rule and figure out just what 1/2 homasote or 2" pink foam gets you.
Decision #2 is: do you elevate everything and then cut away what you don't need? Or do you elelvate only what is high, such as the track and roadbed? Knowing that in advance can avoid a lot of wasted material and difficult cutting. Both homasote and foam can be rather nasty to cut inside the house. At least hot knives and wire work on the foam (remember the ventilation). Even knife blade saws result in dust with homasote. I do all my homasote cutting outside when I can.
Personally on my HO layout set in fairly flat parts of Wisconsin, I found that 1/2 homasote or 5/8" plwyood subroadbed PLUS cork roadbed gave me enough elevation for culverts, lowered sidings, and a modest amount of rolling land so that residential areas will not be pancake flat. For the creek valley and for an excavated underpass in my town I built special and slightly lowered David Barrow-style "domino" segments of benchwork just for those locations.
The Barrow system I use has two grids, the lower one is attached to the legs and it, and the legs, are always the same height, while the upper grid has the plywood top and can vary in height although for most of the layout it is the same height. I think Barrow has simplified the system since his original articles and now uses a single grid but I am pleased with the height flexibility the original system uses, at the cost it is true of using more wood than bare necessity would dictate. Wood was cheaper when I started this thing!
Dave Nelson