Here's a bunch of stuff on ammonia (NH₃) flare design: http://www.google.com/search?sourceid=ie7&q=ammonia+flare+design&rls=com.microsoft:en-us:IE-SearchBox&ie=UTF-8&oe=UTF-8&rlz=1I7ACEW_enUS408US408

And H₂S flare design: http://www.google.com/search?sourceid=ie7&q=h2s+flare+design&rls=com.microsoft:en-us:IE-SearchBox&ie=UTF-8&oe=UTF-8&rlz=1I7ACEW_enUS408US408

Hire a consultant locally.

I expect the volumes of these gases aren't sufficient to warrant hydrogen recovery and recycle to the refinery? As a chemist, I wonder that more isn't done to recover hydrogen. This would especially useful since the by-product should be sulfur (marketable??) and nitrogen (free to the air). I will not pretend to tell you how to undertake this process, and it is much easier to burn both the gases. Once burned, there will be off-gases (air permit, etc.) such as sulfur dioxide, and NOx.