Early permit applications have already been processed, and my unerstanding is that Glacier recieved a large amount of trip requests this year. Do some research, come up with a couple of potential ideas, and see where it takes you from there. Get in touch with the Park Service, let them know of your desired trip length and what you'd like to see, and they should be able to cook something up for you.
I agree with Sushiman that Cutbank will be far and away your best bet to avoid RVs. Also, if you are fortunate enough to land a backpacking itinerary in the North Fork area of the park, you will almost certainly enjoy the primitive car camping sites at Bowman and Kintla lakes. Very quiet, very scenic.