The Nest Heat link normally replaces the programmer (UT2) because that's where the necessary wires are located and the programmer will be redundant once the Nest is installed. The Nest thermostat should be located in the best position in your property so that it controls the heating properly. I've added some tips below.
The original thermostat (RS1) can be left in situ and set to maximum, so that it doesn't interfere with the operation of the Nest, or decommissioned by making a wiring mod to bridge the original thermostat switching circuit thus allowing the old thermostat to be removed.
The Nest thermostat can be connected to the Heat link T1 & T2 terminals for its operating power, or you can use a separate plug in power supply.
Tips for Room Thermostat Location:
The positioning of the room thermostat is critical to the correct operation of the system.
The room thermostat should be in a room that is not effected by other sources of heat such as an open fire, cooking equipment, or direct sunlight etc. It should not be somewhere draughty or too close to a window, especially if it's one that is opened in the winter.
Secondly it should be in a cool room, ideally the last to warm up. That way the other rooms will be warm enough, (but not overheated because of their TRV’s) before the room thermostat switches the entire heating system off.
At least one radiator in the room with the thermostat installed should not have a TRV fitted. Otherwise the TRV may interfere with the correct operation of the room thermostat.
The thermostat should be mounted about 1.5 metres from the floor, and not close to, or above a radiator.
Preferably it should not be on an outside wall, (although if you have well insulated walls, this is not quite so crucial.)
It should be in an area where air can circulate easily, not in a corner, or hidden behind curtains, or furniture.