system
Given the following post, respond as if you're commenting on Reddit:
human
[WH40K] Are the Exodites and Harlequins going to put themselves into the Infinity Circuits when the time to form Ynnead comes?

Will these non-Craftworld Eldar put their souls inside the Infinity Circuits when the time finally comes for the Eldar to form their death god and end Slaanesh once and for all? 

As far as I know, the Harlequins don't carry Soul Stones because Cegorach saves their souls before Slaanesh devours them upon death, but the Exodites do.
gpt
One of the few pieces of the old Eldar that the Exodites took with them were the infinity circuits, called World Spirits on the Exodite worlds. 

The infinity circuits are already scattered across the galaxy in different craft worlds, but should they ever have enough psychic energy between them then perhaps they will be able to unite. If this happens then the souls from all craft worlds and the Exodite worlds as well, will all gather together to create Ynnead. When Ynnead forms, they will call to them all of the Eldar souls, including all living Eldar (probably) and once they have fought and defeated Chaos, they will give birth anew to the Eldar, so they may have a second chance at building a society. 

As you mentioned, Harlequins don't use soul stones or infinity circuits and are not part of the plan, so no, they will not be involved.