Often, the initial part setup is positioned at the same point as the stock axis.

You can position the setup axis at whatever point is convenient for locating part zero, but the stock must be moved so that the stock axis is positioned at the center of rotation of your indexer. This cannot be performed with the Stock step, instead it must be done using the stock properties dialog box as follows:
Select the stock in the graphics window.
Click the Properties
button at the bottom of the screen. The stock properties dialog box comes up.
On the Dimensions page, adjust the X, Y and Z coordinates to move the stock. In the example below, it is assumed that the center of the stock will be aligned with the axis of the indexer. The stock is shifted by a negative amount in Y equal to half the stock width and a positive amount in Z equal to half the stock thickness.

Click the Apply button to see the results.
Click OK when the stock has been moved correctly.