does it blow cold air? or no air? The blower motor squeeking is usually a sign that its on its last leg..
But im not sure why this would have an effect on the way the engine runs.. Does it idle rough? lack power? does this happen exactly when you turn the heater on? Is it overheating? running cool? checked your coolant levels?
The more info you can give, the better idea we can get as to what your problem is