The Bunker allows you to keep Units and Resources safe from enemy attacks. The higher the Level of your Bunker, the more Units and Resources you can keep there.
The capacity of your Bunker is governed a by “Power Limit.” The “Power” of a Unit is equal to the value of its best combat statistic. For example, if a Unit has an Offense value of 8 and a Defense value of 10, its “Power” is also 10, as this is the highest combat statistic.
Thus, if the Bunker has a Power Limit of 1000, it will be able to protect 100 of this Unit.
If you have more Units than you can fit in your Bunker, you will have to evaluate which ones you want to protect and which ones should be left outside to defend your Base.