As the system is still new the best course of action that you have is to call the installing contractor and have them send over a tech to take a look at things and make recommendations. If you're within the first year most times a complaint of operation is covered by a first year labor warranty from the installation company.
Explain, when you call, the problems you're seeing and hopefully the tech will talk with the installers to find out what and why they did what they did during installation.
If you, the homeowner, start experimenting with things like closing off registers etc. you could cause operating problems with the system that won't be covered by warranty and will lead to a possibly expensive service call so they can come out and explain things to you.
Use the biggest hammer you like, pounding a square peg into a round hole does not equal a proper fit.