Do you know the furnace and AC equipment models and sizes?

How large in area are the two zones?

I would have to find out that info- I don't have it on hand. I know we have a Maytag AC (m2100 I think) and some kind of HE furnace. The furnace is in the crawl space and I don't really go down there. Our home is 3500 sq. ft. So I'd say the upstairs is around 1000, and downstairs is 2500. We also had an air filtration system put in place. Not sure if that would make a difference or not. The guys still have one or two things left to do before they're done so we haven't paid the last half of the bill yet so we don't have the warranty info, etc. with model numbers.

I suspect your contractor has installed an furnace and AC that is too big for your duct work. This is what is causing the noise. The condition is aggravated when the second floor zone is calling for heating or cooling. It the zoning is not done properly too much air is going to the second floor duct work which causes even more noise.

Most HVAC contractors are not good at zoning. I hope they have installed a properly sized variable speed furnace and 2-stage AC. If not then it may be difficult to solve the noise problems.

All the equipment you have purchased should have been detailed on your quote. If it was not, then you never received a valid quote.

I suggest you withhold the final payment until the problem is corrected. Gather up all the information and start talking to the contractor.

Thank you for your input. Ugh. I hate hearing that and I hope they have installed the correct equipment. I plan on calling Monday. We'll see what they say.