There are a couple aspects to your situation. There is a tendency for many owners to want their puppy to go from being in the palace overnight to having free run of the house and expect them to return to the palace to eliminate. While this goal can be achieved it takes time, repetition and making the transition from palace to free run gradually, this is best accomplished by using a portable pen or having the palace in a small room so that the puppy is never far away from the pad until they have better control. You can also take the pad and tray with you if you are going to a different part of the house.
Submissive urination fortunately is something that most puppies outgrow. You can try to avoid this problem until he outgrows it by leaving in the enclosed environment long enough to eliminate before you go to him or speak to him. I know it is frustrating but avoiding the triggers that initiate that response is the most reliable way.