I use a rear rack and trunk bag, a frame pack for my tool kit, tubes etc., an under seat bag for phone, keys, wallet and a handlebar bag for misc food items, I also carry 2 water bottles (1 water and 1 gatorade).
I can carry an amazing amount of stuff with this set-up.

I only use a backpack, hydration system when I am mountain biking and the above setup for commuting.