There are 4 DIMM slots to place RAM. Two are controlled by controller 1, the other two are controlled by controller 2. As long as all memory is compatible together you should be fine with 3. You just have one controller with 1024MB and one utilizing 512MB. Also, if it's not the same RAM, but still compatible, it will all be reduced to match the slowest DIMM's speeds.
Just make sure it's compatible.