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This question would be much better if you added your actual URDF.

The robot does not have to be at the origin of your world. In general, you would add a link and joint to place the robot arm in your environment in the correct position. You would then add the rest of the environment objects in the appropriate place, also using links and joints.

And yes, you should add e. g. a box underneath the robot to represent your robot base, to avoid collisions with it.

Remember not to change your robot arm's URDF directly, because it is supplied by UR, but instead to use the macro to add the arm to your own URDF.