I can't recall where I read this, but this is what I do:
Practice new sections first. My mind is fresh and my enthusiasm is highest.
Practice sections which need detailed work..particularly sections which I thought were "done", but upon reflection really aren't (fast "runs", trills, e.g.)
Practice exercises, including scales.
Play through "finished pieces"...I rotate these. It is a nice way of reinforcing that yes, indeed, I can "finish" a piece.
I also use a timer and practice whatever for 15 minutes, then go onto a new section. I find that 15 minutes is about the maximum I can focus on anything before I'm just playing mindlessly.
Good question!