Please note that all bonuses for the Daily Duty Roster are credited to your account automatically right at the moment when you open the game on the corresponding day.
Having entered your Sector, you can see your balance with already added bonus Crystals.
Troops are credited directly into the Bunker. Hence, when you open your Bunker, you can see the number of Battlecruisers etc. with already added bonus units.
Bonus items and resources packs are allocated to the corresponding tabs on the Black Market.