On the iPhone
Within the Keynote Remote app, go to the Settings page. Select “New Keynote Link,” which will give you a new four-digit passcode.
On the iPad
Using the Keynote app on the iPad select the tools icon at the top right of the screen. Next, select Settings and then Remote. Select your iPhone by clicking “Link.” From there, type in the four-digit passcode you received on your handheld.
Now you may control your iPad Keynote presentation using your iPhone!
Take a look at this video, courtesy Nothing But Tablets:
Keep in mind both iDevices must be connected to a Wi-Fi network or have Bluetooth turned on to work.