If you're doing a DEM of the route, I would not substitute portals. In my opinion, that would defeat the purpose of an accurate route. If you really want to go through with the portals though, you will need to do the following:
1) Place at each end of the Cascade Tunnel an asset titled "Portal." The asset is built-in and can be found under the Objects section.
2) Rename each of them to a recognizable name. I would suggest Cascade Tunnel East and Cascade Tunnel West.
3) Open the menu of one portal and check the box: "Train returns after 5 real minutes delay." Another set of options will appear. Check the box that says: "Trainz returns through alternate portal 'none.'" If you opened the East Portal's menu, you would change the return portal to be the name of the west portal.
4) Repeat step three for the other portal.
On a side note, you should start a screenshots thread. I am quite interested in this route being a Great Northern fan.
Cheers!