In Glacier we have done and would highly recommend using the shuttle buses that run very frequently on the Going to the Sun Road - as per Blazing Zipp mentioned these vans
We stayed in our 37ft MH, no toad in St Mary's CG in August couple of years ago on a first come first served basis (knew there was some boondocking locations just outside on the west we could utilize which we did night before). Our schedules change as we travel, based on what interests us longer/shorter in some locations more so than others, so for us we rarely if ever reserve. We had an awesome 4 days covering quite a bit of the park (we are not big hikers, but do enjoy short hikes of interest). St Mary's CG is a short walk over the bridge to the visitor centre to get a shuttle.
Waterton, we were last at just before the fires and it truly was a fantastic visit, which we have done a half dozen times over the years being Albertans. However, there was a major fire which we are led to believe caused a lot of damage, so might be worth double/checking on how things are today there compared to prior. Just saying, and we love the "Peace Parks" as they are affectionately known.
We have only stayed at Lake Louise CG once, and the trains immediately behind, for us were so noisy all night long we only ended up staying one of our pre-booked nights being unable to sleep. Now they also have a huge dry overspill place off the main Hwy for those not able to get in the CG's due to high demand = again just mentioning for you to consider researching into further.
Hypothetically, and to each their own depending on time available and how long you want to explore each but 3 days is way too little to do both Glacier/Waterton & Banff/Lake Louise areas together. If you are Calgary based initially, then maybe head out to Canmore/Banff & Lake Louise for those 3 days.
If however you have a lot more time to enjoy this gorgeous part of the world, do one of two big loops maybe??? = If we were starting at Glacier (3 days), we'd then do Waterton (1or2nights), head up towards Pincher Creek (Walmart there for some groceries), then for us once we hit the Crowsnest Pass we'd head up on the Cowboy Trail then through Hwy 40 (over 2 or 3 days) = Kananaskis Country/Peter Lougheed PP/Spray Lakes all the way to Canmore which is a beautiful little town to explore along the River especially! Also great views of the 3 sisters range = Faith, Hope & Charity. From there you are close to the gate into Banff National Park (2 nights) Lake Louise vicinity inc Johnston Falls/Canyon and other desirables (min of 2/3 nights).
From there if you have the time, maybe head up the Icefields Parkway towards Jasper (lots of beautiful stops enrolee), and cut back across east to Edmonton (Huge Mall!) then south back to Calgary, maybe experiencing slightly east returning, Drumheller Dinosaurs and walking on the moon feeling landscape.
OR Another option, especially if you love some of the most gorgeous lakes and waterfalls .........
East side Glacier National Park then up to Waterton National Park, then onto the Crowsnest Pass HWY 3 heading west. Have brief stops at Lundbreck Falls?, Sparwood Huge Truck?, Fernie O/N maybe and explore town/riverwalks. Next up explore Fort Steele Heritage Town as you head further up Hwy 95 to Golden (so far you would have covered about 366 miles 7hrs driving only from Glacier NP East Side to Golden). From here you would head east on the TransCanada Hwy 16 towards Calgary, going through Yoho National Park (833ft Takakkaw Falls & Wapta Falls), Emerald Lake, Lake Louise (Moraine Lake nearby). From this juncture if time permitted you could either head up the Icefields Parkway HWY 93 towards Jasper checking out Peyto Lake enroute, or go direct east still towards Banff, checking out Johnston Canyon & Falls, Two Jack Lake, Lake Minnewanka, Banff Townsite, then Canmore River/DT and on to West City Limits Calgary. This whole loop without Jasper section from St Mary's Glacier would be approx 10hrs drive time 500miles. Alternatively you could also head south towards Bragg Creek, just prior to City Limits (Pretty area to K' Country and Elbow Falls etc) exiting Calgary on the South side. Going from Lake Louise to Jasper is about 3 half hours 150miles.
Hope the above gives you some ideas/options. FWIW, we rarely book anything in advance, but equally our personalities aren't phased that we wouldn't find somewhere to stay.
We hope you enjoy our country and our home base area as much as we've had the pleasure over the years of enjoying yours.