Where do I put two commas in this sentence: Some women believe it or not fought in the Civil War disguised as men?

The commas must be placed as follows, and I will explain why:

Some women, believe it or not, fought in the Civil War disguised as men. 

"Believe it or not" is what we call a non-essential phrase.  That means that if we took it out of the sentence, we would still have a perfectly good sentence.  We use these non-essential phrases as little modifiers in sentences, to explain or describe something, for example, and they...

The commas must be placed as follows, and I will explain why:

Some women, believe it or not, fought in the Civil War disguised as men. 

"Believe it or not" is what we call a non-essential phrase.  That means that if we took it out of the sentence, we would still have a perfectly good sentence.  We use these non-essential phrases as little modifiers in sentences, to explain or describe something, for example, and they are commonly used, so it is important to understand how they should be punctuated.  When they occur mid-sentence, they are always set off with commas on both sides.  Here are a few examples for you:

Miss Smith, the English teacher, had a reputation for being tough.

The employee, having a broken arm, was trying as best he could to do a better job.

My students, the ones in the history class, are starting a new unit on the Civil War.

In each instance, the words that are between the commas are explaining something.  In each instance, if we took those words between the commas out of the sentences, each sentence would still be a proper sentence. 

We do this because, as the reader is reading, he or she needs to know which groups of words should be processed together in groups, so their meaning is clear. Without the commas, it would be difficult for the reader to know that, and the commas are like road signs, to help navigate the sentence better for clear meaning.