When you replace the motherboard, you need to connect the case cables to the motherboard. If you have never done that before, I recommend using the motherboard's manual to locate the pins. There should be a few pin clusters on the bottom side of the motherboard, I can't be specific since it varies from one to another. The pins usually have labels. Be sure to mind the polarity on the pins, otherwise they won't work.
There should be pins for the front panel audio jack, internal speaker, reset, HDD led and power button.