What do the babies look like? Are they still pink and blind and hairless or are they fuzzy and a bit bigger? If your timeline is right and they really are two weeks old you should be able to take everyone out of the cage and change all the bedding, in and out of the nest, without bothering anyone too much. If they still seem like brand new pinkies I'd leave them alone a bit longer.
Carefresh may not be the best option, it's infamous for causing sneezing. I've never seen any research that shows it actually causes respiratory problems but it does cause sneezing, irritation, and porphyrin, which seems like it would be uncomfortable even if it wasn't technically making them sick.
In just the little nest area, I used to put pieces of fleece, that way you have really soft fabric that feels great to sensitive baby skin but no strings or loose edges that they can get caught or strangled in.