To tunnels, there are 2 common ways to approach it. Either do the cheap and easy way, where you simply make the tunnel go into the actual ground, and use 3ds fog effects to try to hide the ground collision, or you can use some heavy 3ds work, which, if not done carefully, can make it look just horrible, and it's best that newbies stick to the first method. To water, you also need to use 3ds for that as well. Depending on the ride's surroundings and situation, you might have to modify a 3ds water mesh so it tesselates and you can remove surfaces on it to allow the coaster to go below without colliding. Otherwise, if you think covering up the collision with fog effects would work, go ahead. Now to make things easier, you might want to use the tunnel maker to make doing the fog easier. You can use the tunnel maker to create the 3ds tunnel, then go into the 3d modeller and add in the fog from there, it's easier than the tedious (not to mention unreasonably stupid) method of placing and scaling every fog piece inside the NL editor. And if you don't use 3ds tunnels, then you might just have to do a lot of painful guess and check work along with manually placing the fog effects in the editor. (the fog effects you can use is simple, it's basically just a flat, translucent plane, but has a texture on it. You use many of them together to create the gradual effect.