In terms of how they work in the bot, I think they'd be separate chromosomes. That is, their code would be isolated from the rest of the genome and the results of all chromosomes' stores would get combined in some way that doesn't favor plurality. Something like a simple max. That's the same mechanism that I want to use to do diploid, so we can mimic the lifecycles of some fungi that have haploid and diploid alternating generations. A diploid cell would have two "brains" controlling it, and dominant/recessive genes work just by how large of numbers they're storing to sysvars. An infected cell would likewise be controlled by multiple programs, but the programs are largely ignorant of each other and can't directly interfere with each other.