The nest doesn't replace the hot water side of the programmer, that can carry on working as before with no problem.
You can either totally divorce the central heating circuit from the programmer or just set the heating programmer to be ON permanently, then the nest heatlink can be wired to replace the room thermostat, preferably mounted somewhere near the wiring centre.
A photo of the wiring centre insides (with some labels if possible) would be useful if you need more information.
Where will i find the 'Wiring Centre' you speak of jack?