Its really confusing even for those of us who followed the story. As you know there are two Sayorans - one "real" and one clone. There are also two Sakura's one is real and one is clone. Real are together and clones are together. "Real" Sayoran met real Sakura in the past (when they were just little kids) and real Sakura got cursed by Fei wong. To save her life Sayoran traded his freedom to change the past - as result in xxxHolic Wakameki was created as his "replacement" for his parents. Fei Wong captured him and cloned him and put clone with Sakura who was also cloned around the same time. So in the first chapter - you see both clones twice. First page - where they are in tube trying to reach each other (its the future) and the beginning - Sakura loosing her feathers and Sayoran making a deal with the Witch to go after her - ALL CLONES! Then later real Sayoran got free and clone Sayoran turned evil and the team found out that Sakura was a clone when she was killed by Fei Wong. They went to find the real her and clone Sayoran got good again and sacrificed himself to save real Sayoran. Witch got some mojo going on and while Fei Wong was fighting real guys sent clone Sakura and clone Sayoran to alternative past to live out their lives.
BUT Here comes the time paradox: Clone Sakura and clone Sayoran grew up and had a baby boy who IS the "real" Sayoran. So "real" Sayoran is the child of his clone! To save his life - both clone Sayoran and clone Sakura make a deal with the Witch so she could help "real" Sayoran and thus on ch1 page1 you see them in a glass tube - which is Witch's doing! Witch dies so Fei Wong destroys everything because apparently he had done all evil stuff just to save her from dying! (btw in xxxHolic Wakameki takes her place as store owner and makes a "deal" that leaves him eternally young but unable to leave the store - EVER.)
So both Sayorans and both Sakura's get together (clones ages's are reversed so they both teenagers now but they love Sayoran now since he is their only son! Both Sakuras call their feathers and save the world and Fei Wong in the last attempt traps both Sayorans in some dark place from which there is now way out!

As manga goes (not by time in TRC):
1) 1chapter 1page=ending of story. Clone Sakura and Clone Sayoran are in glass room separated by wall. the Dimensional Witch put them there as payment for helping real Sayoran - their son - they are both de-aged and aware that he is their son.
Story starts. Clone Sakura+ Clone Sayoran (don't know each other are clones). First 100-150chapters (2 TV seasons). (we get a hint of real Sayoran captured.
real Sayoran escapes. doesn't know that its clone Sakura - thinks she's real. clone Sayoran turns evil. (OVA - Tokyo Revelations). clone Sakura is now aware that she is a clone, she hides it and still loves clone Sayoran and just OK with real Sayoran.

another 50chapters - collecting feathers fighting with evil clone Sayoran. Fei Wong/evil clone kill clone Sakura and she reveals that she is clone and real one is captured and held in her original world - Clow Country. (OVA - Tsubasa Shunraiki)

They travel to her original world which is stuck in time. real Sayoran tell his story as he and real Sakura fell in love in past- Fei Wong cursed her. real Sayoran failed to save her. Sacrificed his place with his parents and his freedom to turn back time and change it to save real Sakura from curse. He is captured by Fei Wong who clones him and puts a amnesiatic clone Sayoran in his place and clone Sakura - both in past as kids. There is a hint that this might have changed the pasts of Kurogane and Fay (making it real tragic).

Fei Wong starts end of world. Witch Yuko interfaces - as real Sayoran and Sakura fight with Fei Wong, their clones resurrect in real (xxxHolic) world past and grow up. real Sayoran is born (at 10-12) - sent to Witch - who sends him to meet real Sakura who gets cursed. Adult clones sacrifice their freedom to help small Sayoran. Witch traps them in glass tube - ch1p1. Back to present. They escape - their ages go back to become same age as real Sayoran and Sakura but clones know that real Sayoran is their son and want to stop the time loop. real Sayoran meets them and realizes that they are his parents.
2 Sakuras and 2 Sayorans face Fei Wong - end of world - here we are now!
(BTW. Real Sayoran's real name is not Sayoran. His father told him to take his name when talking to Yuko and others)