Your @free.Kindle.com address is exactly the same as your @kindle.com address except for the addition of free.
For example: if your kindle address is:
kin1@kindle.com then your free kindle address would be:
kin1@free.Kindle.com
It is a bit confusing I know and I think Amazon could have done this better somehow.
I can't remember if I use my free address or the standard with Calibre. But the essential thing to know is that unless you are receiving documents via 3G - there should be no charge. That said I do limit my Personal Document Limit on the Manage your Kindle page to zero. That way I won't get charged unless I choose to change it.