Once you have some track down, you can mark sections of it to have special properties. A section can be marked as:
This illustration shows tunnel track (hard to see) connecting levels of the helix in John Armstrong's Southern Pacific Shasta Division, from Model Railroader, Apr 2005:

Each of these properties can be applied only to one or more complete segments of track. To apply a property to a portion of a track segment or curve, you must first isolate that portion by chopping it out, as described next.
To isolate a section of track:
Say you want to isolate the portion of this curve between the hash marks. You can see the full extent of the original curve by highlighting it. Use the Track tool
for this procedure.
1. Draw a straight segment touching the curve where you want the first chop point. 2. When you release, a switch is formed. 3. Repeat, drawing another segment at the other chop point. 4. Point to one segment and press Del. The segment and switch disappear. 5. Repeat for the other segment. 6. A small portion of the original curve is now isolated between two new junctions.
To hide a section of track:

The track is redrawn as a dashed line. Trains passing over this dashed section will appear hidden.
To create a section of tunnel track: the procedure is the same: draw the track or isolate it, right-press and choose Tunnel. When a contiguous series of track segments are marked Tunnel, the train hyperspaces across all of them at once.
To mark a section of track untouchable: same procedure again. Be careful when you use this feature! Once a section is marked untouchable, you can no longer select it, move it, delete it, create a switch or junction in it, change its properties, or connect any other track to it -- it becomes dead. Make sure the track is fully connected and its properties set before you mark it untouchable.
To reenable an untouchable section: right-press any track and choose All Retouchable. This reverts all untouchable track to its normal state. Note: if all tracks are marked untouchable, then you can't right-press any of them; draw a new temporary segment to use the All Retouchable command.