Here the word "brightness" likely refers to the brightness that is often associated with Yahweh's glory. Possible meanings are 1) the brightness of Yahweh's glory was like flashes of lightning or 2) the brightness of Yahweh's glory was like the rising of the sun.
The word "there" refers to Yahweh's hand. Possible meanings are 1) the lightning bolts that Habakkuk can see are only a small representation of the full power that he cannot see hidden in Yahweh's hand or 2) Yahweh hides his power in his hand until he is ready to use it.