If they are 5600 or earlier, the shift cable will come out the side near the front of the lever. If they're 5700, the shift cable will be routed under the bar tape.

It does sound like you probably have 5700, in which case those probably aren't R560 brakes. If they are, that may be your trouble. If the brake is made by Shimano, the part number will be stamped on it somewhere, probably near where the cable attaches.