The small jellyfish-like seeds seen throughout the movie are always said to come from the Tree of Souls, and Quaritch states that it's the Na'vi's most sacred site, presumably meaning it's central to their mythological beliefs. Speaking in terms of species, there doesn't appear to be any difference between the two Trees other than the sheer size of the Tree of Souls, probably indicating more advanced age on its part.
Actually, I believe, personally, that The Tree of Voices is more the Na'Vi ancestors, as Neytiri says, and The Tree of Souls is the "All Mother", the deity...Eywa. but, i could be mistaken..its just the gist i got from it.
The Trees of Voices are always together in a group. I don't know much about their neural connection, and if there's a difference when Na'vi put their queues onto the trees, but the Tree of Souls is one of many "sacred" and scarce trees. I can only guess it has more "info" or a larger place to "store" all of their history and ancestor's voices.