I do it with a good, proven collimator, a pair of Weaver base bottoms and a non adjustable try scope. If it looks like things will line up I will go ahead and fit the base. Then when you screw it down and find out it doesn't line up anymore you can epoxy bed the base to the receiver with the screws barely tightened and make sure it'll work.
Most time if it's a good barrel you can hold the barrel in V blocks, find the edge, and move in to their center. That should put you on center of the receiver, but of course double and triple check everything before you punch the first hole. Once the first screw is in, put the base on and check to make sure it bore sights. Then when it's perfect move over and do another hole. If everything is good the base should be straight now, and the rest of the holes are easy. Just take your time and be careful!
BTW, what kind of rifle are you fitting a rail to that isn't drilled already? That's kind of unusual.