The control scheme is altered for using the zapper. Shooting is done with the trigger, while you look around with the control stick. The buttons on the nunchuk are surprisingly still accessible and needed for swapping weapons. Holding the gun and aiming proved to be awkward at first, and only slightly awkward as we kept playing. Reloading was accomplished by shaking the zapper.
Though the top buttons of the remote were accessible, we found it uncomfortable to do so when we had to hold the A button, the C button on the nunchuk, and then the trigger to lob a grenade (replace trigger for a gun shake to slash with your knife). It works fine, but the feeling of intuitive controls was at that moment lost for us.
For those wondering, the Capcom representative we spoke said the gun was not going to be compatible with Resident Evil 4. The Wii zapper is indeed interesting, but our initial impression using it with Umbrella Chronicles is that it doesn't add that much to what we'd enjoy with simply the remote-nunchuk combination.