I'm guessing you are doing something like this.  
 
Names Default To Here( 1 );
dt.bigclass = Open( "$SAMPLE_DATA/Big Class.JMP" );
New Window( "WAIT!",	
	Beep(),
	V List Box( Text Box( "Manually Add/Delete Rows or Columns In Data Table" ), ), 
	Hlistbox(
		Buttonbox("OK", 
			<<Set Function(
				Function({self}, 
					print("do stuff");
					self<<Close Window;
				)
			)
			
		)
	)
);
print("this shouldn't show until okay");
// other stuff
where you don't want the "this shouldn't show until okay
 
You need to not do ANYTHING else until okay is pressed though.  The normal way I do this is by using functions and calling them from the okay button.  
 
Names Default To Here( 1 );
dt.bigclass = Open( "$SAMPLE_DATA/Big Class.JMP" );
action_okay = function({}, 
	//{DEFAULT LOCAL}, //uncomment this if you want the variables to be local only (don't exist outside the function)
	// put everything you want to do after okay button in here.  
	print("this shouldn't show until okay");
	// other stuff
);
New Window( "WAIT!",	
	Beep(),
	V List Box( Text Box( "Manually Add/Delete Rows or Columns In Data Table" ), ), 
	Hlistbox(
		Buttonbox("OK", 
			<<Set Function(
				Function({self}, 
					print("do stuff");
					action_okay();
					self<<Close Window;
				)
			)
			
		)
	)
);