Deadlifts work the traps, so it's no surprise that you get sore there. If you need more trap work, it's OK to do after deadlifts, or on another day if you like. It's really hard to overwork your traps.
As far as back training, I think most will advise you to do the deads early in the training session, so you are not too tired to maintain proper form, and keep the reps low as well for the same reason. You will not "interfere" with other muscle training, although you may have to reduce volume on some lifts on deadlift days. I currently will do deadlifts on every other back day because as they are so taxing, about once every week and a half or so is all I can handle, and it gives me a day to move other back training to primary on my non-deadlift days.