Hi Terry,
The first step is pretty simple but very important as it sets the axis for the whole thing and that is to get the First face cut square with main shaft axis once that is done then everything is set from that surface. To do this I set it in the 4 jaw roughly where it should be, get the centre on the face marked where the input shaft will go and then adjust the chuck so the live centre in the tailstock is lined up. then with that held by the tailstock I readjust the chuck end so that the five relevant surfaces ( Top, Bottom, both side plate, and the B/H surface) are level and I use a sprit level to do this, then I face off the B/H surface. From this point on everything will be square to that surface. I hope that makes it a little clearer, I'm quite sure if it were being done in a flash state of the art machine shop they would have some fandangle laser beam show to do it all but I don't have that so it a case of measure, check, remeasure and recheck.
Cheers Leon