It all depends how you're going to run the system. If you check pages 42 and 43 of the installation guide, you'll find some sample systems. Will you be fitting a HR92 to every radiator, or having the entire home controlled as a single heating zone plus a hot water zone?
It would also be useful to know how you are using your current system. You have a 2 channel programmer and also a 7 day programmable thermostat. You presumably aren't using the timeclock on both of these - do you leave the heating channel on the programmer set to always on, and then use the thermostat as the heating timeclock? Again, this would be useful to know to allow us to work out how your existing wiring centre is being used.
Finally, a picture of inside the wiring centre would also be helpful. There's a definite way the 42005748-001 should be wired, but that doesn't necessarily mean that your original installed did the job correctly :P