Where do I input deductions to my house for health reason, such as taking up carpet and cleaning air ducts?

Medical expenses are an itemized deduction and only an amount of total medical expenses greater than 7.5 percent of AGI can be deducted. 

I have been treated for allergies for a while. I had my air ducts cleaned to help with the allergy.   Do I need something in writing from the doctor or is the fact that I'm being treated enough to take this deduction?

Yes, you would need to have something in writing from your dr. saying this was a medically necessary thing to do. 

You will only get a benefit from this if your total itemized deductions are greater than your standard deduction and only from the medical expenses that are greater than 7.5% of your AGI.   

Itemized expenses include mortgage interest, state and local taxes up to $10,000, medical expenses in excess of 7.5% of your AGI. .