If it's better to run multiple generators in sync with the same frequency/program or have each generator running a different one?

Neither. Whenever you read a Protocol where multiple generators are running the same Preset (or Program) you'll see that the generators are started with a larger time difference than the dwell time for that setup. This time delay (offset) is to keep the same frequency from running on multiple generators simultaneously.

The purpose of running the same program on more than one generator with the offset is to get a very rapid repeat of the same frequency so any damaged pathogens are hit immediately again.

There are trade-offs both ways. Some people have many small problems, so running different programs on each generator makes more sense. Some Protocols focus on one thing at a time, while others focus on hitting multiple things at once.

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