Yes you can, but only one by one.
Select the block with the new material.
Then "Transform block tool" and click at the block you want transform.
But careful, you basicly could transform your Tritanium crew quarter into a Naonite armor.
I wouldn't be able to transform a crew quarter into a nap items armor block, because at least in my client the armor blocks etc does not exist for me in naonite, the base armor block nor the armor corners or armor slope exist I'm my building mode, but I've seen enemy ships with them.