This is an answer before the question is asked, and was prompted by a little article in an engineering mag that Darren brought our attention to in a very recent post about pistons, and a request for help on another website I frequent.
A couple of quick and dirty methods of aligning the tailstock.
This first one uses a DTI (not a clock gauge) held in the chuck.
http://www.gadgetbuilder.com/Lathe_Align.html#Tailstock_AlignWith this next one, you place the rule against the spindle centre and gently bring the tailstock one to meet it. Depending which way the rule deflects, depends which way the tailstock needs to be moved. You really need to keep the tailstock spindle as short as possible for accuracy's sake. This method is also used to get your cutting tooling to the correct centre height, but you use the side of a bar in the chuck, and move the tool towards the bar with the ruler between.
For doing the tailstock alignment you should have the centre mounted into the headstock spindle. If you can't do that, mount a piece of bar in your chuck and cut a sharp pointed taper of around 60 degs using your topslide. Once this has been used, and taken out of the chuck, it cannot be reused until a new taper is cut on the end.
This method can also be used from the side, to see if your tailstock is at the correct height. But adjusting that out is rather a more complex operation.

As I said, these are a couple of quick and dirty methods that will get you very close.
The correct method is to make up a test bar when you first get the lathe and driving between centres a cut is taken at each end of the bar. This allows for perfect alignment, and the test bar will most probably last the life of the machine.

If the disk at the tailstock end is larger than the headstock end, then the tailstock needs to be moved towards the operator, and the opposite if it is smaller. Keep moving the tailstock and taking a very fine cut until both are the same. The tailstock is then perfectly aligned.
I hope that this has helped.
John
I forgot to add, if I am turning tapers with an offset tailstock (very rarely), I always drill the centre holes with what is called a radiused centre drill, it allows the centres to sit slightly offset without binding. Our John Stevenson actually uses a ball bearing in place of the normal centre, it does the same sort of thing.
