I would not do that. I would just go ahead and remove the older thermal pad, place the arctic silver directly onto the main chip and then put the low profile heatsink on it.
If you put the paste right on the pad and then the heatsink on that, it's not going to do much. The heat transfer will be much better if you remove the pad. Worst case scenario, it gets too hot, you can put the pad back on, or buy replacement pads.