Wow! Shop manager you say? Tough position. I am guessing none of the machinists working there know anything. Right? Have you set up a manual lathe before? Indicating is the best way to align the center of the spindle with the center of the tool. Do you know which offset to change? Do you know how to change it? Do you have all the manuals there? Have you read through them? Are all of the turret locations off zero position?
Normally on a lathe when using a center cutting tool (i.e. drill) the X offset for that tool should read 0.0000. Does yours read 0.0000. If not, what happens to the tool position when you set it to 0.0000?