Rachel,
When you use whether to introduce a phrase that isn't essential to the meaning of the sentence then that whole phrase is set off with a comma.
I like all foods, whether it's Chinese or Mexican
We will still have the yard sale, whether it's raining or shining.
It depends on whether or not it's raining outside - that expression is vital to the meaning of the sentence and is not set off by a comma.
I hope this helps!