i watched the dubbed version of Yu-Gi-Oh GX when it was on TV, and the last episode they showed was when Jaden defeated Yubel and was told that he was some prince from another world who was sent away because of some darkness. He then enters a portal with Yubel to confront it, leaving his friends behind.
Is that the end of the series, or does it continue off somewhere (like maybe linking to a season of 5D's another Yu-Gi-Oh Series)?
The Yu-gi-oh! GX dub by 4Kids ends after the defeat of Yubel, which is in episode 155. This is the 3rd main arc in the anime, the Dimension World Arc (Note that 156, while still belonging to this arc, was never dubbed). However, there is one more arc of the anime which was never dubbed in English, which is just called Season 4. The conclusion of season 4 (episode 180) is the end of the Yu-gi-oh! GX anime, and the story isn't directly continued in any of the other series, apart from the special "Yu-Gi-Oh! 3D: Bonds Beyond Time" which features the main characters of the main series, GX, and 5D's. So to answer your question, yes, the GX anime continues for another 25 episodes after that point.
There's also the manga, which is very different from the anime. It's more like a continuation of the original Yu-Gi-Oh! TV series and manga, and a lot of things are changed in the plot. It's also worth noting that the anime actually predates the manga in this case.
While I've linked to Wikipedia articles above, you can find the same information at the Yu-Gi-Oh! Wiki entry for GX, as well as a lot more information which is not on Wikipedia.
