In general, work from larger muscle groups to smaller. But there are always exceptions. Some people do "push-pull" workouts, working opposing muscle groups together: Back-Chest, Quad-Ham, Bi-Tri, etc. Shoulders are kind of on their own there.
For most of my 2 days per week clients, I have them do shoulders on lower body day because it's really hard to fit back, chest, shoulders, bi's and tri's into one workout. You can get a good lower body workout done in 45-50 minutes which leaves 10-15 minutes for shoulders, which is more time than they'd get if you tried to wedge them into upper body day. Just my opinion.
When you switch to a 4 day split, you'll see even better results with a pyramid training scheme
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