2nd Yu-Gi-Oh! movie

http://www.animefreak.tv

Sure GX is on there. I remember seeing it on Youtube too. I finished GX, so I can criticize it. Had I not finished it, I wouldn't bother to. GX was really crappy..

EDIT: Oh, it's on there. Just checked, all episodes of GX are up.

Errr....I've already seen all of GX, I meant the movie. Sorry, should've been more specific. XD

Er, no. When he fuses with what's-his-name or something before fighting the 2-colored eyes monster. When his eye-color changes, it means his monster + him fuses. It's sorta weird. He fuses spiritually like.. twice in the anime, and it's almost in the same season. It's rather annoying and confusing.

Err...-Must correct-
Jaden never "fused" with someone until he fights Yubel. He contained the energy of an ancient ruler and became "The Supreme King". He then later fights Yubel, with whom he fuses his body, becoming part Yubel, part Jaden. This gives him the "abilities" of Yubel, but also causes his eye colors to change temporarily.
The ancestor thing you were talking about refers to the fact that Jaden is the reincarnation of Haou, a prince from Neo Space. The ruler, Haou, was chosen for The Supreme King's power, so Yubel was there to protect him as he learned to control his powers.