You won't have any big mountains in Montana if you take I-94 to I-90. Hwy 2 from Minnesota is a very pleasant way to go into Montana.
There are so many crossings...just choose depending where you want to travel. Here's a list of the crossings. Note that they all have different hours of operation. We used Sumas, Washington east of Seattle on the way up and returned to Roosville, Montana just west of Glacier on our return. All the crossings went smoothly and fast. Just answer only their questions is a word or two. Don't offer information. Take off your sunglasses, greet them and look them in the eye and you won't have any problems.
One thing I'd recommend is to not do a lot of siteseeing in the lower 48 on your way or you might be worn out before you cross into Canada. There is just so much to see in Canada, the Yukon and Alaska. Upon your return, if you still have energy left then do the lower 48 siteseeing.
Ooops...I just reread your post and you want to hit Banff as your first major stop. Traveling as long as you can in the lower 48 will save you money in fuel prices. Roosville, Montana would be a good crossing for you for Banff. We stopped at Jasper/Banff on our return and that's why we crossed at Roosville.