I suppose the easiest method which is likely owned by most people is a digital caliper. If you hold one jaw on the ball screw and have the other on the outside of one rail, you can then measure at varing positions to get it running in line. You would likely be best to have a shim of some sort between the jaw and the ballscrew so that you are sure you are not measuring slightly in one of the ball tracks. If you then get one rail set that way and then the other then that should get things aligned pretty close.
Of course that method will only work if you are sure the ball screw is actually in line in the first place, so it may mean you have to readjust the whole lot a second time.
What I think I would do is set it up as described and then place a Clock (DTI) on the base with its needle against the Z then raise the slide and see if the needle stays constant, if not then it shows you need to adjust the whole lot again to offset things.
Hood