This isn't meant to sound like a smart ass, but just do the exercises correctly. Many people don't really focus on their technique and end up becoming upper trap dominant in their movement. If you are already UT dominant, you really have to focus on technique during the exercises.
For Prone Ys:
- stop using weight for now if you are, until you properly activate the lower traps and can raise your arm without UT dominance.
- make sure you are performing them with your forehead resting on something; your upper traps will be activated if you have to hold your head up (like in this video http://www.youtube.com/watch?v=GAApeDY_yiM&feature=related) and it will be harder to minimize their recruitment during the Y raise.
A few other exercises I like are the reach roll and lift off the wall and off the floor. The wall will be a good starting place since you are not going against gravity, then progress to the floor.
You can also try SMFR/trigger point work of your UTs to decrease tonicity prior to performing the lower trap work.