Depends. First off, I have to ask so I apologize, did you indicate the rotary table? You state it was centered. Also there are some things you may not realize. This is easiest done in a lathe, but it can be done in a mill. You have to indicate the rotary table, taking into account WHICH direction you last moved the table to get t either the X or Y axis to zero. This is because if you don't, the slop in your table will NEVER allow you to get the hole back in the center. I say never, but I digress, everyone gets lucky once in a while. Sorry for babbling, but in my mind I can do this in my sleep but to describe it in words that are easy for others to understand can be challenging. Once you see my description you will understand why this is best done in a lathe..
Ok, so you must indicate the rotary table, you have to know which direction you moved the table last as that is the direction with NO slop. This needs noted for the X and the Y axis.
Then mount the 3 jaw must be centered to that same point AND with the table being last moved in the same direction as the rotary table. That is gonna be tough.
Let me change the entire course.... Try this...
Buy a piece of .25 stock, using a small V-block, clamp it in a good strong vise mounted to your table, Indicate the .25 stock to zero, lock the table from movement, you will be centered, then drill your hole, done... You will have so much hair left over....hope this helps...
(EDIT)And if you don't have a good V-block or a vise, use your 3 jaw chuck clamped to the table and indicate the .25 material in there, will work just as well.