If your brakes are squealing with the carbon rims, you will need to adjust the toe-in of the brake pads. An easy way to do this is to fold a business card in half and place it behind the rear portion of the brake pad. Squeeze the brakes against the rim and tighten. Now the front half of the brake pad will be angled towards the rim and your wheels won't be screaming at you.
theres not a lot you can do - its one of those minor niggles, should go away on its on. You can clean the pads down and remove any grime thats in there.
double check the wear on your pads as well as carbon specific pads wear quite quickly as well
You may also want to look at this re 'toe in' http://www.boydcycling.com/maintenance/