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Jay Connor wrote: ...if I wanted a 3:1 ratio, and I wanted to knock down the brightness of the bottom light (and maintain its distance from the subject) does anyone have any suggestions other than using a neutral density gel on the bottom light...
The Jule rating indicates the amount of power going into the flash tube (more-or-less), but it doesn't indicate the amount of light falling on your subject.
As others have said, it depends on what modifiers, reflectors, etc. are mounted. If your top light is in a high-output beauty dish and your bottom light is in a double-diffused soft box the ratio on the subject will be very different than if both lights were in standard reflectors.
You can eyeball test shots to get the look you want, but as was also said, if you want precise ratios a flash meter will be essential.