My suggestion is that we set a reference resolution to work in; so if you're targeting the iPad's native resolution but also want to run on the iphone, you'd do something like so:
[[CCDirector sharedDirector] setReferenceResolution:ccp(1024, 768)];
...
[mySprite setPosition:ccp(100,100)];
If I understood correctly the feature, I think it wouldn't work when the code is already resolution independent.
For example:
[[CCDirector sharedDirector] setReferenceResolution:ccp(1024, 768)];
// I use this code in a lot of places
CGSize s = [[CCDirector sharedDirector] winSize];
...
[mySprite setPosition:ccp(s.width/2, s.height/2)];
On the iPad it will place the sprite at (512,768),
but on the iPhone it will place the sprite at (120,80) (actually I don't know if I did the math correctly) and not at (240,160).
If people want the reference-resolution feature (this means loading bigger images in iPhone which might not always be possible since 2nd generation devices supports up to 1024x1024 textures while 3rd generation (and possible the iPad) supports up to 2048x2048 textures), I would be cheaper to scale down the game.
Something like this:
scale factor = device_resolution / reference_resolution;
[scene setScale:scale_factor];
// if you are scaling down the game, don't forget to generate mipmap images.
IMHO, the game would look better if users have 2 different sets of images: high res images for ipad, low res images for iPhone.