We drove to GC from Flagstaff by way of Cameron Trading post, where we had lunch. Very easy drive which takes you the Navaho Reservation, nice lunch, and great souvenir shopping. At Grand Canyon, these lodges are in a row: El Tovar, Kachina, Thunderbird, Bright Angel. El Tovar is the epitome of the old fashioned log hunting lodge with a buffalo head, elk, etc. Very atmospheric. We stayed in Thunderbird and had dinner at El Tovar, for which you can make reservations online 30 days out, then breakfast at the original Fred Harvey restaurant in the Bright Angel.
The Red Route shuttle stop is outside Bright Angel and it makes about 9 or so stops at lookouts into the canyon on the way up to the last stop, Hermit’s Rest. You get a brochure describing the stops (5,000 foot drop overlook, etc.). You get off at the stops you pick and then take the next shuttle, which run about every 10 minutes. Coming back from Hermits Rest takes about 35 minutes. If you would like to hike between stops, there is one paved section about a mile long - ask the driver which stops it is between.

As as far as staying in Sedona, we used Marriot points at the excellent Courtyard which is in a gorgeous red rock setting a bit out of town. The drive from GC to Sedona on 89A is not for anybody who fears drop offs. Very mountainous, twisty, slow, no shoulder...max speed 35 MPH, or 20 or even 15 on the curves. But scenic.

If I were you coming from Phoenix, I would not make Sedona an overnight, just a drive through the red rock country. We stayed in Flagstaff at the Hilton Garden, which is very nice and usefully located right next to a Coco’s Cafe for an easy, inexpensive dinner for tired travelers.