Missoula is a good central location. Keep in the mind the railroad is split between Paradise, MT and Missoula, MT. There is a river route along the Clark Fork River and a Evaro Hill route up and over. Trains can run either route depending on MOW, other train movements, tonnage and horsepower. On the eastern end, Blossburg Tunnel area is really cool although you might need 4 wheel drive to get up and around in this area. I don't think they plow the forest service much. Also MRL runs manned helpers to push heavy trains up and over pass through Blossburg Tunnel. They usually cut on at Helena for westbound trains and disconnect at Elliston, MT (reverse for eastbounds). Last time I was up there they were using HelperLink technology so they just cut off on the fly, pretty cool. Having a timetable with milepost locations is very handy. If you don't already have one check out this MRL's website here
http://www.montanarail.com/station_bysub.php
They list mileposts out by station with siding lengths and yard locations as well. It isn't as comprehensive as an Altamont Timetable, but it is better than nothing.
As for trains, most of the traffic on the MRL is run through BNSF trains. There are several manifest trains that terminate/originate in Pasco, WA such as the PASLAU, PASKCK, or PASFTW (and counterparts). Also probably see loaded grain and coal trains coming from Eastern MT, WY, and the midwest to points along the west coast (don't forget the empty counterparts). You might catch an occasional stack or auto train either the V-PTLKCK or possibly something else. As for MRL traffic there is a day and night "gas" train out of Missoula up to a plant near Thompson Falls, MT (I think this train runs weekdays only??). There are Laurel-Missoula and Missoula-Laurel trains that run too, although I am not sure on their frequency.
Here is the MRL frequency list.
Montana Rail Link
160.335 Channel 1 - Road
160.950 Channel 2 - Road
160.395 Channel 3 - Yard Switch
160.380 and 160.950 Channel 4 - Blossburg Tunnel
160.545 and 161.130 Channel 5 - MRAS
161.340 Channel 6 - MOW
160.245 and 161.490 Channel 7 - MRAS
160.830 and 161.355 Channel 8 - MRAS
161.385 and 160.815 Channel 9 - MRAS
Have a safe trip and enjoy it! Beautiful country to railfan although traffic can be slow sometimes so have patience.
Marlin