Clerestory windows should either be placed on the north or south side of the house. They aren't usually placed on the east or west unless there are clerestory windows on all for walls of the house on the outside.

How high should clerestory windows?

To maximize the effect of clerestory windows, they should be located facing thermal mass walls, at a distance of between 1 and 1.5 times the target wall height. So for a 12-foot wall, the clerestories should be 12-18 feet away.

Which direction should clerestory windows face?

The windows are typically operable windows and best oriented either south or north. A south-facing clerestory requires adequate roof overhang to prevent direct solar gain. Operable windows in the clerestory also allow heat to escape from the house during the cooling season.