I'd imagine separate, because assume you wish to use the original release and have nothing to do with the revisions within the Ultimate Spheres of Power.
In that case, the newer version with undesired changes, is in conflict with your version.
Let's also assume that my group would like the newer version, as we like the changes.
Several of the existing talents have disappeared (such as Greater Blast, within Destruction) and several talents have been wrapped into other talents so you get more bang for buck (such as Greater Healing
natural bodybuilders each combined with various condition cure talents, instead of being stand alone talents).
If my group is using the newer version, we don't want Greater Healing (as stand alone talents) or Greater Blast (at all... since it seems to have been removed for balance(?) or some other reason).
I couldn't really see the practicality of one file and a toggle option for whether to use the old or the new.
The Ultimate files will be quite a bit of coding, and were sold as part of the kickstarter (and will be available for purchase eventually, I'd assume).
In addition to some people having bought both, it will likely be easier to code and maintain them as separate sets of files.
The original files will likely be unchanging (unless a future Hero Lab release breaks something).
The new files could potentially be subject to errata, but any changes to Spheres as a system would be to the current/most recent iteration.
We don't have our hard covers yet, so are still using the original system (and I'm buying the older files, as they're released) with hero lab.
I'd imagine a lot of the existing stuff would serve as a framework for the new system, but that there will still be significant effort to create the new files.
Adam, on the kickstarter page and in answer to someone's question, said the new files are being worked on but that he has no ETA.