"who has bigger margins ... pepsi or the bottlers?"
Pepsi without a doubt. Same with Coke and CCE.
CCE (the Coke Bottler spun off and held in almost majority by Coke) had dismal returns for the first few years. Every time they held price and started to make money, dispite losing sales, Coke would step in and force them to drop price and gain back sales (lower CCE margins, greater Coke margins). The CCE dividend was a nickle and didn't change for I can't remember.
Pepsi and Coke look at the bottlers as necessary evils.
I will say that, thanks to the programs we developed for them, the Pepsi and one Mountain Dew Bottlers increased their margins over what the Coke bottlers made.