@galactus3000,
 
Which JMP platform are you using Fit Y by X or something else? Off the top of my head, if using Fit Y by X, I would use a custom script to add the data filter and add to it a Data Filter Handler. That is a bit involved.
 
If you are using Graph Builder to draw your boxplots, you can right click in the X-Axis (group axis) and select which Order by Statistic, default is the mean, and Select which Y variable to order by either ascending or desending.
 
The script below opens the JMP sample data table SATByYear.jmp and creates a Graph Builder boxplot of SAT Math vs. State with a Local Data Filter for Region.  Now select one or several regions and ordering is updated automatically. Change from descending to ascending.  You can do all of this voa point & click.
 
I hope this meets your needs.
 
Names Default to Here(1);
dt = Open("$Sample_data/SATByYear.jmp");
gb = dt << Graph Builder(
	Size( 534, 464 ),
	Show Control Panel( 0 ),
	Variables(
		X( :State, Order By( :SAT Math, Descending, Order Statistic( "Mean" ) ) ),
		Y( :SAT Math )
	),
	Elements( Box Plot( X, Y, Legend( 6 ) ) ),
	Local Data Filter(
		Add Filter(
			columns( :Region ),
			Display( :Region, Size( 160, 120 ), List Display )
		)
	)
);
   