When you click the "Auto Schedule..." button from the scheduling window, you are initially presented with two options.  Click the "Show more options..." button to see all of the different ways the auto scheduler can be run.  To schedule just one job, choose the option that says "All empty positions in just particular jobs..." and then click the "Continue" button.

The next screen will ask you to specify the jobs you want to schedule by selecting them.  You can also limit the shifts that will be auto-scheduled by clicking the button that says "Limit shifts as well...", or to schedule these jobs across all of your shifts, just click the "Commence Scheduling" button.

The auto scheduler will only fill in those positions you specify, and at a later time, you can always go back and have the auto scheduler fill in the remaining empty positions by clicking on "Auto Schedule..." in the upper right hand side of the scheduling window once more.