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Sam, perhaps it's too ambitious to let both Zillions versions
participate. You could decide which of the two versions that should
participate by playing a game or two between them. You would find that
the tweaked version tries to control the centre with the pawns, that
it more often castles, etc. The untweaked version will spend much time
jumping about with the knights and  super-knights. So the tweaked
version should participate in the tournament and the other left out.
In the tournament, Zillions will probably only achieve a draw, at
most, but this doesn't matter if it plays good and interesting chess.
These are factors which have been tragically left out of computer
chess. This is on account of the inferior understanding of chess among
chess programmers. They are experts in algorithms, but not in chess.
In the tournament result one should also weigh such factors as
seemingly intelligent and creative play. Today, programs like Rybka
are very sophisticated. But historically the focusing on the result
implied that it was only the bean counting capacity that carried
weight. The program that succeeded in counting beyond the other
programs' move horizon was always the one which won the tournament.
However, a program that made positional pawn sacrifices, or made
daring pawn storms on the wing, etc. counted as nothing. So these
tournaments only make sense if one not only looks at the result but
also takes into account whether the programs manage to play fine
chess. /Mats