I would use the cork on the Main line. and put the track right down on the foam for the "Mill track"
Thats the way to go!
The mainline would be raised on a ballast bed, while the siding would be lower. It might be slightly raised (you can buy thin (1/8") sheet cork at craft stores and WaMart that can be cut to fit) and then it will have some small drainage ditches on the sides (just carve a small ditch into the foam). Also, use some scrap foam or maybe some carpenters wedges (those wooden wedges they use to mount doos and windows) will make the ramp to go from the main to the siding smoothly.
That's the way to do it if you want to use the cork.
Me, I took a little different approach that has worked well. It may offer some food for thought for you.
When building my current layout I was looking for a cheaper alternative to the foam roadbed I used last time and with none of the drawbacks associated with cork (it dries out and gets hard and brittle as well as acting like a noise amplifier when it gets that way). As I was walking through the local home improvement store I spotted something that might work, and even better, it was out of season so it was on sale!
I use a foam base with my roadbed and track secured by the latex caulk. For roadbed I use rope caulking. It comes in a roll about 15' long, and it's perfect width for HO scale track right out of the box. Since I model N, I just tear it along the already formed centerline and I get about 30' of roadbed per box with no waste. The advantages are that it never dries out, so it's always soft and pliable (absorbs sound!), it can easily be molded to any curve radius you want, it's easy to cut with just a xacto knife to form turnout pads, crossovers and such, or you can use a wallpaper roller on it to flatten it and make trasitions in rail heights or lower passing sidings in just a few seconds. As if that isn't enough, the latex caulk holds well to it, but you can still slip a putty knife in there and take up the rails without damage if you need (Spread the caulk very thin with a putty knife when you lay it down and then lay the tracks and use some canned goods laid lenthwise along the tracks to hold it while it sets up). If you get it in the off season like me you can often find it for a buck or two a box. It comes in gray and brown that I've seen, though other brands may come in other colors.
Here's what I bought...........
http://i83.photobucket.com/albums/j319/pcarrell/Autumns Ridge/Picture016.jpg
http://i83.photobucket.com/albums/j319/pcarrell/Autumns Ridge/Picture019.jpg
http://i83.photobucket.com/albums/j319/pcarrell/Autumns Ridge/Picture023.jpg
http://i83.photobucket.com/albums/j319/pcarrell/Autumns Ridge/Picture021.jpg
http://i83.photobucket.com/albums/j319/pcarrell/Autumns Ridge/Picture024.jpg
http://i83.photobucket.com/albums/j319/pcarrell/Autumns Ridge/Picture002.jpg
http://i83.photobucket.com/albums/j319/pcarrell/Autumns Ridge/7-15-077.jpg
Hope this helps. It doesn't answer your question directly, but it does give you options.
