You learn something, how to drive a car for example. In the beginning it was difficult and it took a lot of 'conscious' attention. You got really good at this, and it became easy enough, to let your new part take care of it, so that you could text on your phone. You got in the back seat and let the part start doing the work for you. Your hands stopped listening to you, and started listening to this part giving them directions under your authority.
Pain existed with the role and purpose of signaling you when something bad is happening to your body. Since you were born, pain has ran with this programming that you need constant signal to be notified something is wrong, even after you became aware of it. Now that you're older, pain sees you as the same age as you were then. Ask pain if it can trust you enough to not send a signal. Does it believe you have the skills to address your injury seriously without the pain? what happens when you make that agreement that pain can stop and you can address it without the pain? for me the pain disappears.
Conflicts come about constantly. Your parts make generalizations about the world, (which arent always true). They are just like people. Miscommunications happen, Some parts of you think one thing is the case while other parts of you think its the opposite.