I'm fairly sure this is a series, or at least more than 1 book. I remember bits and pieces. There is a space ship, I think it's family run and is a cargo ship. There is an alien race that I think is described as smelling like cinnamon. There is an amorphous entity tied to one of the aliens. The alien dies and the entity is forced to bond with a human male. They have a hard time adjusting to each other but the entity facilitates the ship to go faster/navigate better or some such benefit.
Either late in that book, or later in the series, if it is a series, the human ship ends up in a region of space where they get "stuck". Their engines either don't work or can't get free of the space. Come to find out that region of space is a giant entity that used to be bonded to the amorphous entity that bonded with the human. The space entity teaches the bonded entity how to release the human without killing him. The 2 entities go off together.
I think I read this back in high school, so between 2000-2004, but the book may be older, I don't know.