The reason you are unable to understand this is because you perceive the external world through the sense organs God has given you. You have not yet started looking within yourself. You are seeing the external world. You are not even aware that there is a universe within, waiting for your discovery.

As long as a room is in darkness, you will not be aware of its contents. Light a candle, and you will be able to see all the objects, including yourself. If you throw open a window, your external surroundings, the lawn, the river nearby, the sky, all these become visible. Just because you had not seen them earlier does not mean they did not exist. You have made an attempt only now.

God is always present.

It is only when you start perceiving Him that you know He is, always.