I decided to update my question, just in case someone comes back to look at this asking the same question I was.
I'm using joystick encoders instead of a keyboard encoder. What I found is that retroarch allows you to setup a mouse for use with the game. So my trackball goes in as mouse 1. Since I do not have a UI running on my setup, I don't actually need mouse buttons. I only need the trackball input for the games.
What all this means is that the retroarch setup will use a joystick along side the trackball... meaning the buttons going through the joystick controller work along side the track ball and I don't need extra buttong for left and right mouse clicks.