Start your design with the basic area you want the tunnels or underground caves as a wide area. You can adjust the tunnels a little later.
http://isaacwolfheart.deviantart.com/art/FH-MAP-1-327160301?ga_submit=10%3A1347650459I used the basic grey as the normal ground level, just to show it can be done without using a lighter grey first. Don't change the Mask, when you have everything in order,
go about detailing the Mask.png.
Now that it is loaded in Map Maker, on Width and Height, the trick is changing Height. It's at 300, I normally put it at 900. You can change this to make deeper tunnels.
Turn on the ocean. Ocean Height is 50.
In my map, I am able to go to 140 before it floods my 'cave' and 'tunnel' areas at 150. So I'm setting it at that. I don't like the drop to the rivers,
so I'm reopening the grey scale terrain.png and accenting the rivers in dark greys.
If you want a larger map, change 5000 to a larger size, it will help with the distance between river and caves. It will also accent the rivers in softer terrain levels.
When you're done, add the ceiling to the tunnels. Use plateaus or caves, it depends on size and what materials you have available.
Now try it out. Have fun, make mistakes and see what you get.
My finished Terrain map.
http://isaacwolfheart.deviantart.com/art/FH-Map-1-327160750?ga_submit=10%3A1347650632
