I grew up in the area, Kalispell is a branchline, you probably won't see much action, you should take a short drive up to Whitefish or Columbia Falls, which is the BNSF mainline. In Columbia Falls the RR , the Highway and Flathead River share a canyon. Very scenic, your not too far from Essex Montana. Someone else may pipe in with more info, I haven't visited for years and things may have changed.
In Missoula, the MRL is pretty much along the river, and runs along I-90 both directions. The yard is easily visible off of the interstate. If you travel east on I-90 past Bonner the MRL will be on your right side, you will also notice the Milwaukee Road abandoned ROW travels besides the MRL row ( then the NP ) . Neat stuff, tunnels, bridges, and the abandonded Milwaukee Road substation. This portion of MILW was electrified from Harlowton MT to Avery Idaho. Fort Missoula has some railroad displays, including a Shay Steam engine and Milw Road Station.
In addition, there is a NP ( MRL ) branchline that goes north out of Missoula up the canyon along Hwy 93 towards Polson, not much traffic but an impressive bridge crossing a valley. Keep an eye out for it, it will be on the right side of the hwy if you are traveling north up the canyon.
Here is a link to another board post concerning Missoula, the person was basically looking at Milwaukee Road artifacts but there is some MRL and directions in the post.
http://www.trainboard.com/grapevine/showthread.php?t=91203
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