All your Items (with the exception of Crafting Equipment and Parts) that you've received as rewards or have purchased one way or another will be held in your inventory. You can chose a time to use any of the items there at your convenience. The Items inventory doesn't have a limit so don't worry about missing out on something. The filters will help you out to find everything as quickly as possible and they are as follows:
Economy - Resource crates, Resource Production Boosters and Science Points Boosters.
Base – General XP Boost, Extra Workforce Boost, Satellite Jammer and Peace Shields and General Skills Reset.
Army – Army Boosters for Attack, Defense, Mobility, PvE and Gathering, as well as March Recall and Battle Retreat items.
Utilities – Includes VIP Points, VIP Activation and Speed-up items that can help building, recruiting, researching, crafting or healing activities. You can also buy a Name Change and Avatar Change items.
Crates - Crates of random resources or crafting parts.