I think it's only for the black tank because it would not be as effective if it flushed both black and gray tanks at the same time. Besides, the gray tank normally doesn't receive anywhere near the amount of solids as the black tank does.
You should always drain (and optionally flush) the black tank first, then empty the gray.
However, if you're still unsure, check your owner's manual or contact Jayco Customer Service and ask them.
Can't find what you're looking on JOF? Try:Jayco Owners Forum Custom Google Search
TV: 2009 GMC Sierra 2500HD | Crew Cab | Std. Box | 4WD | Duramax/Allison
RV: 2000 Jayco Eagle 266 | FBS | TT -- 1986 Coleman Laramie pop-up -- Still in the family!!!