I've also had the impression from things I've read (I don't have the sorces, sorry) that Carlos really didn't get much training directly with Maeda, though I hadn't heard that he ever trained with any of Maeda's other students (though, if what I read was true, then the supplemental training makes the most sense).
As far as diffences between the family sides, from what I've seen and read it seems to me that every Gracie has very strong personalities, and don't seem to shy away from self promotion. Basically they all want you to believe that they all have the authentic Jiu-Jitsu... but in the end it is all Brazilian Jiu-Jitsu. What I've seen is the only real difference is that Rorion and the Torrance Academy have choosen to differenciate themselves by focusing on self-defense stuff, and that Rorion's other brothers, though their lineage compete more than Torrence academy students, also tend to put more of an emphasis on the self-defense stuff. That isn't to say that the Gracie Barra, and Carlson Gracie academies don't do self-defense, just that it is less of a selling point with them.
As far as tracing differences back to Helio and Carlos, I just don't think there were any differences. I think this whole thing about Helio being weak, and having to alter the techniques for a smaller weaker physique is a bunch of BS. Most of the pictures we see of Helio are either of an old man, or a man in his 40's and 50's. Ever seen a picture of him in his 20's? While not a monster of a man, it would be hard to claim that he was weak and frail.
Check these pics:
http://www.flickr.com/photos/50544904@N08/4749381727/
http://tonyferraz.files.wordpress.com/2009/09/heliojovem.jpg
If your google-jitsu is good you could probably find a pdf copy of Yukio Tani's 1906 book "The Game of Jujitsu" (Tani taught Jujitsu in England, so it's aa great early Jujitsu text written in English). Guess what, that was published well before Carlos ever took his first Jiu-Jitsu lesson from Maeda, and really I don't see much different between the philosophy and technique espoused in that book with the early Brazilian Jiu-Jitsu. Maeda, from my understanding, traveled Europe with Tani doing prize fights. I suspect that what Maeda taught the Gracies was very close to what is in that book.
*edit*
Here is a picture of Helio and Carlos, and to me Carlos looks like the smaller and weaker...
http://dynamicmma.com/wp-content/uploads/2009/03/carlos_gracie_family.jpg
Also, if you want good basic info on Jiu-Jitsu inovators and competitors check out BJJHEROES.COM it's a really good reference site.
1st generation Jiu-Jitsu fighters:
Carlos Sr.:
http://www.bjjheroes.com/bjj-fighters/carlos-gracie-sr-profile
Oswaldo Gracie (Ha! There is mention of training with Jacinto Ferro after Maeda left in this Bio! Interesting, hadn't read this yet):
http://www.bjjheroes.com/featured/oswaldo-gracie
Gastao Gracie Filho:
http://www.bjjheroes.com/bjj-fighters/gastao-gracie
George Gracie (to me the most interesting of the 1st generation):
http://www.bjjheroes.com/bjj-fighters/george-gracie-facts-and-bio
Helio Gracie:
http://www.bjjheroes.com/bjj-fighters/helio-gracie
Oswaldo Fadda (not really 1st generation as his instructor was Luis Franca):
http://www.bjjheroes.com/bjj-fighters/oswaldo-fadda-facts-and-bio