You need to re-shoot. Put a full screen solid color background image up on the pad (green or blue for keying) and also add some markers (in red) in the corners for tracking. With that, replacing the screen will be easy as proverbial pie...
If you don't re-shoot you'll have to roto the shot. I actuall have had better results with this kind of screen replacement using roto techniques and tracking in Mocha than with keying.
If you do reshoot you have 3 options, none of which require tracking marks to be stuck on the screen. The edge of the device is more than adequate for tracking.
The first option is to leave the screen black with the iPad turned off. The advantage here is that you'll have a reflection of the finger moving over the screen that you can coposite on with the replacement screen to make the shot more belivable.
The second option is to turn on the device and load a still image of the replaced screen on the screen. The advantage here is that the light coming from the screen will light up the underside of the hand, provide some rim lighting and make it easier to sell the shot. It will be more difficult to get a belivable reflection with this technique.
The last option is to load up a full screen full colored area to be used as a keyed background. The advantage here is that you don't have to do any rotoscoping. The disadvantage is that you'll have color spill on the fingers that is coming from a color source very close to the fingers and it's going to be hard to get rid of it. You'll also have the problem of working around any reflections or changes in the color that come from moving the iPad around while filming. It will also be almost impossible to pull a usable reflection of the fingers. Using a colored sheet of paper attached to the screen may reduce some of the color problems with the matte but it will introduce other problems.
For me, and I've done several of these, I always get the best results filming with the device off and using Mocha for tracking and roto. I've tried color keying three or four times but have never been completely satisfied with the result.
Take a look at THIS Mocha/AE/FCP tutorial on screen replacement. It will get you started. This tutorial exports the data to Final Cut but you can as easily save the data for After Effects. Once you get the tracking and roto down you can take a look at THIS totorial which will give you some ideas on how to get the Mocha data and mask into AE.
If you go the chromakey route, check out this app: http://itunes.apple.com/us/app/keeme/id356116160?mt=8
And I've gotten some pretty good fake reflections by copying the hand layer, offsetting a little bit, and using a really high median filter. It erases the fingernails, but keeps the lighting contours.