Yes, the incline does work shoulders. I find it interesting that you are doing both on the same day. I never work shoulders and chest on the same day, just so that my shoulders don't get spent. I work shoulders traps and calves one day and usually save chest for a day by it self.
I do regular straight chest press machine for warmup, light weight, 3 sets, then go to hammer strength incline for 6 or so sets, increasing the weight until I can only get 3-5 reps. Then I do decline where available but if not, I'll do some bench press to the neck on the smith machine. Be careful with this movement, it can kill you. Also, it will pack some serious meat on your upper chest, be ready for that.
I finish with flys or pec dec.
Remember, stimulate the muscles to grow then GET OUT OF THE GYM!!