Please note that all bonuses for the Daily Crew Roster are credited to your account automatically right at the moment when you open the game on the corresponding day.
Having entered your Haven, you can see your balance with already added bonus Rubies.
Troops are credited directly into the Harbor. Hence, when you open your Harbor, you can see the number of Juggernauts etc. with already added bonus units.
Bonus items and resources packs are allocated to the corresponding tabs on the Smuggler's Den.