Here is the answer to my question.
Since I was thinking about using two cases I think it's good to cover both in case someone needs the answer in the future.
If you have the same setup as the movie_review corpus - several folders labeled in the same way you would like your labels to be called and containing the training data you can use this.
reader = CategorizedPlaintextCorpusReader('~/MainFolder/', r'.*.txt', cat_pattern=r'(w+)/*')
The other approach that I was considering is putting everything in a single folder and naming the files 0_neg.txt, 0_pos.txt, 1_neg.txt etc. The code for your reader should look something like:
reader = CategorizedPlaintextCorpusReader('~/MainFolder/', r'.*.txt', cat_pattern=r'd+_(w+).txt')
I hope that this would help someone in the future.
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