My hardwood floor where it meets the carpet in the living room is about 1/2 inch higher than the carpet.. If the base boards continue straight and level from hardwood to carpet then the base boards are 1/2 inch above the carpet.
Depending how much baseboard you are putting down, you can rip a half inch off the basboard that goes on the higher floor, or add a half inch to the bottom of the board that goes on the lower floor. I have done both. If you do the second, you need to fill and sand the joint, then paint it so it doesn't show. This could be a lot of work!