Keep the letters and personal statement as separate as possible, but tell your letter writers what your plans are, especially in the backup specialty. If one is way more competitive than the other, don't tell all your letter writers in the competitive one that you're dual-applying, but discuss it with your mentor(s).
No program will see where else you applied, but if you apply to two different specialties at the same institution, and especially if you interview with both programs, word might get around. And yes, technically they're not allowed to ask, but in many competitive specialties the rules of the match are flouted more often than not. You should expect to be asked about where else you've applied and interviewed, whether you're dual-applying, what you would do if you don't match, etc. at every interview. It's up to you how to respond, but if you want to match, you should answer truthfully and/or tactfully.
