Being Legal on the GDT
The GDT is not a trail like the PCT where you can get a free permit to hike the entire thing, camp wherever you want, except for the few times when National Parks restrict camping at certain areas. The Canadians seem to be obsessive with permits and fees, and I cannot tell what they go toward. Certainly not trail maintenance on the whole or nice campsites or facilities at the campsites. Navigating the permit system seems daunting, but it is really rather simple.
In order to enter a national park, you have to pay a user fee. Since GDT hikers do not enter the parks anywhere near a road or a fee station, it is best (and cheaper) to buy an annual pass to the Rocky Mountain Parks, which include all the ones on the GDT. Cost was about $45. If you wish to camp in the backcountry, you must do so in designated sites and pay a fee, except in places where random camping is allowed. I could not drag out of Parks Canada where these places were, but the Guidebook indicates some of these areas. You still have to pay a fee, though. It works out to be cheaper to buy an annual wilderness pass, which covers all of your per-night camping fees for one year. This costs about $53. The problem is, you still need a wilderness permit, which you are supposed to pick up before you begin your trip. Additionally, you cannot self register. Why? Because you have to make a reservation before you can get the permit (supposedly to limit the number of people who enter into the vast confines of Jasper and Banff). And, you have to pay a fee for each reservation you make. The wilderness pass doesn't cover this cost.
Options for the Thruhiker
There are several options available to the thruhiker of the GDT, from completely legal, to morally legal, to completely illegal. To be completely legal and pay the least amount of money, take advantage of something Parks Canada does not advertise: If you make reservations less than 24 hours in advance, you don't have to pay reservation fees. So, buy an annual entry pass and an annual wilderness pass. Before you leave for the trail (say, in Calgary where there is a big Parks Canada headquarters) make three or four reservations for sites in Banff. Make your best guesses. Warden's will understand (if you happen to see the elusive creature in the backcountry) if you are off by a day or two. When you get to Waterton, stop in and make reservations for the one or two nights you'll be in the park. The reservations are free since it is less than 24 hours in advance. You shouldn't have problems with sites filling up unless you try this in August. You can get around the reservations completely by camping in Akamina Provincial Park, which charges $5 a night, first come - first served. Once you clear Waterton, you will not need reservations until you hit Banff, quite a ways to the north. Note that to camp in Peter Lougheed, you need reservations, but the chances are unlikely you'll camp there: It is less than a half day from Mount Sarrail campground (front country) in Peter Lougheed to its boundary with Heights of the Rockies Provincial Park, where there are no fees and no established campsites. Then, you reach Banff and use the reservations you made back at the start. When you make it to Field, there is a Parks Canada building where you can make more reservations (free again since they are less than 24 hours in advance). Once you reach Jasper, you can make another booking at the Parks Canada office in town.
I followed the above recipe up to Field and then decided not to bother with reservations. From Field, you quickly leave Yoho National Park and enter into forestry reserve land until breaking back into Banff at Howse Pass. This area of Banff is barely maintained and you can random camp here anyways (your wilderness pass covers the camping fees). If you follow the GDT after the Crossing, you hit areas of Jasper where you can random camp (and so you do not need reservations), at least until you make it to Nigel Pass. If you road walk on HWY 93, then you'll have to stealth it or camp in a front country site until you reach Nigel Pass trail. The southern end of Jasper isn't very well traveled, although the first few miles to Jonas Shoulder can be busy. Both Boulder Creek and Four Points camps were fairly full, but there is enough space to squeak by (again, I didn't see any wardens and you've already paid Parks Canada for camping by buying the wilderness pass). After Jonas Shoulder, I saw about six hikers all the way to the Skyline trail, which is the most popular trail in the park. Forget about getting reservations on the trail. Instead, you could try to reserve Trapper Creek camp which is 6 K before the start of the Skyline and was empty when I was there. Then, traverse most of the Skyline to Signal Mountain camp, which is about 12 K from the end of the Skyline and is not super attractive, being that it sits on an old road. It isn't very popular and you should be able to get reservations here. After Jasper, there shouldn't be any problems. I didn't bother to make reservations after Banff (and as I was 2 days ahead when I went through, I didn't use them) and be completely legal because I felt that I had already paid for the camping (wilderness pass), the campsites were mostly dumps (one generally reserves a good thing), there were few people in the backcountry (no competition for space), and I had yet to see a warden in the backcountry. Knowing the Skyline would be busy (it really wasn't - I met 26 hikers over the 35 K length), I took steps to camp at established sites where I knew that I would not be taking anyones spot who did make a reservation. Had Signal Mountain been full, I would have pushed on to the trailhead. Given what I know now, I would still buy the entry and wilderness passes, make one reservation in Banff (Howard Douglas Lake) and use Mount Assiniboine Provincial Park to camp in.
So, we have a second option: Pay all the money you have to, forgo most reservations, plan for the Skyline, and plead for mercy if a warden catches you camping without a reservation; they should be understanding once they hear your story. Stealth camping is, of course, possible. A third option is to pay nothing and just show up. You will probably be fine and meet no rangers. Of course, I cannot ethically recommend this and the choice is yours.