Double Outlet, Half Hot, 3-way Switch
This isn't a hard situation. My preferred approach would be to run power into the first switch 3-way box and 12/3 or 14/3 with ground from that one to the other 3-way switch. Then run the switched cable to both ceiling boxes. That takes care of the switched outlets. Then run a 12/2 or 14/2 with grnd to the ceiling outlet boxes from the first 3-way switch box from the hot, before the switch, to both ceiling boxes. That takes care of the always hot outlets.
I like running power into the first of the 3 way switch, /3 to the next 3 way and from there to the fixture boxes.   That way there is no &quot;code taping involved&quot; and pretty straight forward.
Essentially you are going to have to treat this as 2 circuits.  One for the 3-way switched outlets and the other typical outlet connections in parallel from one to the other.