The program should calculate the Income (Loss) per books based upon the information you entered. Some of these are entered on Schedule K on page 3 of Form 1120-S. For example, if you have cash charitable contributions on your books, they are not entered as an expense on your 1120-S. They are entered on Schedule K line 12a. The contributions will be on the Form(s) K-1 for entry on personal tax return. They will also flow to worksheet that calculates amounts for Schedule M-1. If you want to make an entry directly on Schedule M-1 or the M-1 Worksheet, you can do so by going to Forms mode (by clicking Forms in the upper right hand corner of your screen) and then selecting Form 1120S p3-5 or Sch M-1 Wks under Forms in My Return