Whether you put the desired radial at the top or the bottom has no effect on the needle being centered when you are on the radial. What does make a difference is whether the needle will be directional for the heading you are flying or not.
For instance, if you were to fly the 180 radial (south of the station) inbound on a course of 360 and put 180 at the top of the CDI, you would find that the needle would be non-directional. That is, if it indicated a deviation to the left, you would turn right to intercept the radial or if indicating to the right, you would turn left to intercept the radial.
On the other hand, if you put 360 at the top (and 180 at the bottom), you would find that the needle was directional. If indicating off to the right, you would turn right to intercept.
A phrase I used when learning about radial intercepts and tracking is to say "If I were to fly heading X, the needle will tell me what direction the desired course is from my position" In the xase of the example given above, I would say, "If I were to fly course 360 (as is necessary to track the 180 inbound), the needle will tell me what direction the 360 course is from my position." X is what you put at the top of the CDI to get directional information for the course you want to fly.