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Here are some answers, happy to clarify if needed:
MultizoneWithoutDistribution will only use the pressure network solver to compute the airflows directly between zones and not the distribution system while MultizoneWithDistribution will compute the direct movement and the movement through ducts etc. of the distribution system. MultizoneWithDistribution requires a great deal more input, so unless you're interested in the computing the duct flows rather than just taking what E+ gives you, I'd advise MultizoneWithoutDistribution (at least to start with).
Yes, you can do that. You should use whatever element you can that best matches your need. We don't have an explicit object that is formulated as an orifice with a discharge coefficient, but the crack object can reinterpreted into something pretty close to the orifice equation here (it may be off by a factor of the square root of density, but that's not a huge deal).
You should really only use the reference conditions object if you have measurements of crack properties under non-standard conditions. In this case, the default that gets used (E+ will assume standard conditions if you don't include a reference conditions object) is likely to be good enough.