I use them as the base game does, but with one major difference that I've recently been playing with making an official part of my multiverse's lore:
Siberys, Eberron, and Khyber are all avatars of Sardior, Bahamut, and Tiamat (in their respective orders). I had to do a gender-swap on Eberron for it to work, but otherwise I thought it fit well.
Khyber and Tiamat are both fiendish dragons, the mother of fierce, mighty monsters, and a dark god/god-like figure that wishes to rule the world and escape her imprisonment. They're draconic queens of evil that have followings of deranged cultists attempting to free them from their captivity, as well as being the creator of many fiends.
Eberron and Bahamut are both at least equal in power to their evil counterpart (Khyber and Tiamat), which is how they were able to stop Tiamat/Khyber from destroying/ruling the world for so long. Bahamut is a god of
balance and protection, and Eberron made her sacrifice in order to balance out the world that Eberron takes place in and works to protect the races that live on her. Bahamut can't kill Tiamat anymore than Eberron could kill Khyber, so the only way to stop her was to imprison her.
Siberys and Sardior are both god-like draconic entities that are lesser than the other two (based on the fact that Khyber was able to kill Siberys, and that Sardior and Gem Dragons are less important than Bahamut, Tiamat, and the rest of the True Dragons), are connected to psionics and magical crystals in some way (Siberys as the source of Siberys Dragonshards, which enhance psionic powers, and Sardior as a god of the psionic gem dragons), and being connected to extraplanetary objects (Siberys through the Ring of Siberys orbiting the planet of Eberron, and Sardior through the
Ruby Palace).
Furthermore, due to this bit of lore recently being officialized by Fizban's Treasury of Dragons, Tiamat and Bahamut created the Material Plane of Existence, just as Khyber and Eberron created the world of Eberron.
Additionally, as, in my Eberron, the 3 Progenitor Dragons are/were merely avatars of the 3 Core Draconic Deities, so their deaths in the world of Eberron didn't affect the aspects of the deities in the rest of the multiverse's worlds.
Any thoughts?