Why CMD+N opened new popup Terminal window doesn't follow the default preference? I love Mac terminal in Dark and had set up the default color scheme to a dark one. Every time I open the terminal it's OK but I found that if I open one terminal window and then open another one via CMD+N the new one still remains in the original white one.

How can I make sure every Terminal window I opened all in the default preferences?

I am using OS X 10.9.1.
If I understand the question correctly, this is an easily doable through normal terminal preferences.
Go to terminal>preferences>startup 
Here you can set the default behavior regarding window color scheme, including what color scheme new windows use.