I have flown West Jet with DS many times. If there is an extra seat they will move passengers so they don't have to sit beside you. I have never used the car seat in the extra seat though. I highly doubt they will save you a seat on a plane for free if you book early.
I have done a 5 hr flight with DS 3 or 4 times now with no issues. He loves to move so there was lots of walking up and down the aisles. Over night flights were fine too. The humming of the engine and the darkness made for a good sleep
And in response to 2009baby poop statement: The flight attendant told me it is super common for poop explosions on airplanes. It's something to do with the air pressure change making them poop like crazy.