How do I prepare for a postdoc position with requirements in working with the theoretical basis of the software, which I have never worked with?
Three quick thoughts:


Discuss it with your advisor. They might know of more suitable positions, or have field-specific advice.
During your PhD (and before), you should have improved the skill of learning things on your own. This will be useful in a postdoc or maybe an industrial position. Just don't be afraid to use it.
It seems you have some time left before the defense. Use it to start learning the software and skills you need. Consider starting a new research project where you'd have to use these methods (nothing like learning by doing!), or just reimplementing an existing paper.


Good luck!