The Seek Compact housing is designed to sit horizontally when connected to the bottom of a compatible smartphone. Unfortunately rotating the image isn't an easy fix, because it would mean taking a landscape image and squeezing it into a portrait space (or vice versa).
We are looking into possible hardware or software changes to better accommodate users with side USB ports, but don't have any details at this time.
In the meantime, we recommend something that has been a popular solution with other side port users. A short USB adapter cable allows independent positioning of the camera regardless of the orientation of the USB port.