I have a laptop that had thermal pads on the gpu memory that ended up getting damaged while i was taking it apart to replace the thermal compound on the actual gpu chipset. I was wondering if i could just use thermal compound instead of buying new pads and if so how should i do it?
You can replace thermal pads with apropriate thermal paste which is designed to replace thermal pads. Normal thermal pastes should be of high viscocity in order to cover only the very small gaps between the CPU (or other hot component) and the heat sink so there should be in no way as thermal pad replacement. A thermal paste that is designed to replace thermal pads should be very gummy in order to cover big gaps and of very high thermal conductivity. There is one called K5-PRO which is designed for iMac computers but should be fine for any other computer. You can find videos of it on youtube http://www.youtube.com/watch?v=e9v5MDivZfc
The thermal pads were used because they don't spread over the edge of the chip onto the PCB so you can use thermal compound but you don't need to spread it just put a small dab in the middle and let the pressure of the fan unit spread it.
thermal pads work better when you don't have a lot of control over the gap between the chip and the "heatsink" surface, like some SSDs (between chips and case). if the surfaces of the memory chips are at the exact same height as the main GPU chip, then yeah you can use paste. but if they're noticeably shorter, then pads would be better.