Попробуйте:
myViewController = [[MyViewController alloc] init];
[myViewController setMyCoolFirstArgument: coolArgument];
[myViewController setMyCoolSecondArgument: coolSecondArgument];
[window setRootViewController: myViewController];
и в MyViewController.h
@property (nonatomic, retain) CoolArgument *myCoolFirstArgument;
@property (nonatomic, retain) CoolArgument *myCoolSecondArgument;
и в MyViewController.m
@synthesize myCoolFirstArgument, myCoolSecondArgument;