It depends, if the floor covering lets heat through more readily than the surface underneath the pipes.
Have a look at the heat transmission values of the floor and compare it with the space under the pipes. You don't say whether the suspended floor is a first floor with a ceiling underneath or a ground floor with a void underneath?
If its a void the chances are you will loose a lot of heat through the underfloor exterior ventialtion grills. If its a 1st floor, floor, some ceilings can take the heat other's can't it depends, but the heat may radiate both ways, once again it depends on the value of each material.
Just think of yourself as a btu and you want to escape the easiest way possible, if you can work that out then that is where you put the insulation, to stop it escaping.