insulation between floor and unheated basement

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Severals years ago I had an addition built as an 'apartment" for my mother as she was no longer able to live alone. I decided that i might as well build a basement under a portion of the addition as a safe room (live in Oklahoma, lots of tornados).The water heater was placed in the basement and the bathroom was constructed just above. The floors in the entire addition are always cold in the winter and when I checked there is no insulation under the floors anywhere, even though I stressed to the builder that I wanted EVERYTHING insulated.
The basement is roughed in with dry wall on two of the walls and ceiling. I believe the joist are 2x12. How is the best way to insulate both in between the basement ceiling and floor and underneath the house. There is a min. of 3 ft clearance in the crawl space underneath the entire addition.