How to expand the storage memory on the Yún

I would like some clarification, although the answer may be painfully obvious: What exactly is moved on to the new root partition that you create? Is it only the files that you yourself create, or does it move other important files as well? In other words, in the future, what would I need to do if I lose the SD card or need to use a larger one?

EDIT: jessemonroy650, your probably right. I'll post/research in the future if I need to