I think the problem is going to be HOW to write these entries.
Fleisher treated his book as a sort of biography, with Superman portrayed as one man who went active in 1938 and stayed on the job until 1964. Thus the Superman who met the Legion was the same one who fought the Ultra-Humanite, and so on.
I don't see anyway to handle the multiple Earths concept without undoing this basic premise of the Great Superman Book, and editing Fleisher's original entries to reflect what happened to which guy.
The same way Fleisher handled contradictions. Just note them.
That's why in the Multiverse entry I stated that "some Superman historians" believe that the earliest Superman chronciles are actually the history of the earth-2 Superman.
Some of these issues are simply unresolvable. We can't pretend that the earth-2 Superman is that same is the Earth-1 Superman because the two have met.
But we can't pretend that the Earth-2 Superman is the Golden-age Superman because that leads to its own set of contradictions (earth-1/earth-2 crossover point anyone?)
The ambiguity has to simply be incorperated into the database because it exist in the chronicles.
Personally, I'd prefer the articles to be written from a real world point of view. To me that makes the issue easy to deal with.
But the ambiguity can still be dealt with when writing from the point of view that Superman is in fact real. Just write articles from the point of view that some of the chronicles may be inaccurate or disputed and when neccessary include both sides of a contradictory issue as if it's something that "historian" are themselves fighting over.