Here is a cool website which shows you how to index cubic structures easily. Non cubic structures are more complicated and you usually have to measure d-spacings to find the zone axis of the incident beam, and then simulate the diffraction with some software such as crystal maker to see if you get the same pattern. Crystal Maker is really good because you can upload CIF file from the American Mineral Database.
If you need more detailed instructions for indexing non cubic electron patterns, just let me know. Cheers.