That depends on the type of cooler you get. Generally speaking there are two types.
This:
This:
This one could act as air intake but I would not recommend it. This is because the air that comes in is heated up by the HDD. I would recommend installing a proper air intake fan or do what I have done and install a CD bay intake fan:
Yeh, its best to have a dedicated fan as an intake. And its usually better to not be right near the HDD cos it will get heated up a lot. What case do you have?